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Li B, Zhang Y, Liu X, Zhang Z, Zhuang S, Zhong X, Chen W, Hong Y, Mo P, Lin S, Wang S, Yu C. Traditional Chinese medicine Pien-Tze-Huang ameliorates LPS-induced sepsis through bile acid-mediated activation of TGR5-STAT3-A20 signalling. J Pharm Anal 2024; 14:100915. [PMID: 38634065 PMCID: PMC11019283 DOI: 10.1016/j.jpha.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 11/22/2023] [Accepted: 12/07/2023] [Indexed: 04/19/2024] Open
Abstract
Pien Tze Huang (PZH), a class I nationally protected traditional Chinese medicine (TCM), has been used to treat liver diseases such as hepatitis; however, the effect of PZH on the progression of sepsis is unknown. Here, we reported that PZH attenuated lipopolysaccharide (LPS)-induced sepsis in mice and reduced LPS-induced production of proinflammatory cytokines in macrophages by inhibiting the activation of mitogen-activated protein kinase (MAPK) and nuclear factor-kappa B (NF-κB) signalling. Mechanistically, PZH stimulated signal transducer and activator of transcription 3 (STAT3) phosphorylation to induce the expression of A20, which could inhibit the activation of NF-κB and MAPK signalling. Knockdown of the bile acid (BA) receptor G protein-coupled bile acid receptor 1 (TGR5) in macrophages abolished the effects of PZH on STAT3 phosphorylation and A20 induction, as well as the LPS-induced inflammatory response, suggesting that BAs in PZH may mediate its anti-inflammatory effects by activating TGR5. Consistently, deprivation of BAs in PZH by cholestyramine resin reduced the effects of PZH on the expression of phosphorylated-STAT3 and A20, the activation of NF-κB and MAPK signalling, and the production of proinflammatory cytokines, whereas the addition of BAs to cholestyramine resin-treated PZH partially restored the inhibitory effects on the production of proinflammatory cytokines. Overall, our study identifies BAs as the effective components in PZH that activate TGR5-STAT3-A20 signalling to ameliorate LPS-induced sepsis.
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Affiliation(s)
- Bei Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yong Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xinyuan Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Ziyang Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shuqing Zhuang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xiaoli Zhong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Wenbo Chen
- Department of Cardiology, Xiamen Key Laboratory of Cardiac Electrophysiology, Xiamen Institute of Cardiovascular Diseases, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Yilin Hong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Pingli Mo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shuhai Lin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shicong Wang
- Fujian Pien Tze Huang Enterprise Key Laboratory of Natural Medicine Research and Development, Zhangzhou, China
| | - Chundong Yu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
- Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
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Li P, Zhang Y, Zhao C, Jiang M. Evolution of the Tóxicos en Levadura 63 (TL63) gene family in plants and functional characterization of Arabidopsis thaliana TL63 under oxidative stress. PLANTA 2023; 258:87. [PMID: 37750983 DOI: 10.1007/s00425-023-04243-8] [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: 07/09/2023] [Accepted: 09/13/2023] [Indexed: 09/27/2023]
Abstract
MAIN CONCLUSION TL63 orthologs were angiosperm specific and had undergone motifs loss and gain, and increased purifying selection. AtTL63 was involved in the response of yeast and Arabidopsis plants to oxidative stress. The Tóxicos en Levadura (TL) family, a class of E3 ubiquitin ligases with typical RING-H2 type zinc finger structure, plays a pivotal role in mediating physiological processes and responding to stress in plants. However, the evolution and function of TL63 remain unclear. In this study, TL63 homologs were dated roughly back to the origin of land plants and confirmed to have subjected to the gain and loss of motifs and increased purifying selection. Phylogenetic analysis displayed that 279 TL63s could be divided into four main clades (Clade A-D). Notably, the ancestral tandem TL40/41 cluster contributed to the expansion of modern Brassicaceae TL40/41. The substitution rate tests revealed that the TL63 lineage was evidently different from other lineages. The codon usage index exhibited that monocotyledons preferred to use not A3s and T3s, but C3s, G3s, CAI, CBI and Fop. Sequence analysis showed that the TL63 homologs had conserved TM and GLD motifs and RING-H2 domain whose key amino acid residues accounted for the high average abundance. Particularly, Arabidopsis thaliana TL63 (AtTL63) was located in the nuclei, cell membranes and peroxisomes and expressed universally and significantly throughout A. thaliana development. Under H2O2 treatment, low or moderate expression of the AtTL63 held beneficial effects on the growth and viability of yeast cells and the mutation or overexpression of the AtTL63 positively affected the growth of A. thaliana plants. In brief, this study could supply useful insight into the evolution of the plant TL63s and the AtTL63 functions under oxidative stress.
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Affiliation(s)
- Peng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yuxin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Changling Zhao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China.
| | - Min Jiang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
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Movahedi A, Wei H, Kadkhodaei S, Sun W, Zhuge Q, Yang L, Xu C. CRISPR-mediated genome editing in poplar issued by efficient transformation. FRONTIERS IN PLANT SCIENCE 2023; 14:1159615. [PMID: 37139106 PMCID: PMC10149819 DOI: 10.3389/fpls.2023.1159615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/23/2023] [Indexed: 05/05/2023]
Abstract
Background CRISPR has been increasingly used for plant genetic improvements because of its high efficiency and precision. Recently, the authors have reported the possibility of homology-directed repair (HDR) using CRISPR/Cas9 through woody plants such as poplar. HDR often replaces nucleotides with one donor DNA template (DDT), including homologous sequences. Methods CRISPR-Cas9 was recruited, and three variables, Agrobacteria inoculator concentration, pDDT/pgRNA ratio, and homologous arm length, were designed to integrate nptII and 2XCamV 35S into the MKK2 promoter zone. Results Here, we showed that recovered poplars on kanamycin-supplemented media exhibited enhanced expression of MKK2 affected by the precise integration of 2XcamV 35S and nptII, improving biochemical and phenotypic properties. Our findings confirmed that Agrobacterium inoculator OD600 = 2.5, increased DDT numbers during cell division to 4:1 pDDT/pgRNA, and optimized homologous arms 700 bp caused efficient HDR and increased MKK2 expression. Conclusion Efficient transformations resulted from optimized variables, directly affecting the HDR efficiency through woody plants such as poplar.
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Affiliation(s)
- Ali Movahedi
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- College of Arts and Sciences, Arlington International University, Wilmington, DE, United States
| | - Hui Wei
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China
| | - Saeid Kadkhodaei
- Agricultural Biotechnology Research Institute of Iran, Isfahan Branch, Agricultural Research, Education and Extension Organization, Isfahan, Iran
| | - Weibo Sun
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Qiang Zhuge
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Liming Yang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Chen Xu
- Nanjing Key Laboratory of Quality and Safety of Agricultural Product, Nanjing Xiaozhuang University, Nanjing, China
- *Correspondence: Chen Xu,
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Lv P, Zhang C, Xie P, Yang X, El-Sheikh MA, Hefft DI, Ahmad P, Zhao T, Bhat JA. Genome-Wide Identification and Expression Analyses of the Chitinase Gene Family in Response to White Mold and Drought Stress in Soybean (Glycine max). Life (Basel) 2022; 12:life12091340. [PMID: 36143377 PMCID: PMC9504482 DOI: 10.3390/life12091340] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/16/2022] [Accepted: 08/23/2022] [Indexed: 11/30/2022] Open
Abstract
Chitinases are enzymes catalyzing the hydrolysis of chitin that are present on the cell wall of fungal pathogens. Here, we identified and characterized the chitinase gene family in cultivated soybean (Glycine max L.) across the whole genome. A total of 38 chitinase genes were identified in the whole genome of soybean. Phylogenetic analysis of these chitinases classified them into five separate clusters, I–V. From a broader view, the I–V classes of chitinases are basically divided into two mega-groups (X and Y), and these two big groups have evolved independently. In addition, the chitinases were unevenly and randomly distributed in 17 of the total 20 chromosomes of soybean, and the majority of these chitinase genes contained few introns (≤2). Synteny and duplication analysis showed the major role of tandem duplication in the expansion of the chitinase gene family in soybean. Promoter analysis identified multiple cis-regulatory elements involved in the biotic and abiotic stress response in the upstream regions (1.5 kb) of chitinase genes. Furthermore, qRT-PCR analysis showed that pathogenic and drought stress treatment significantly induces the up-regulation of chitinase genes belonging to specific classes at different time intervals, which further verifies their function in the plant stress response. Hence, both in silico and qRT-PCR analysis revealed the important role of the chitinases in multiple plant defense responses. However, there is a need for extensive research efforts to elucidate the detailed function of chitinase in various plant stresses. In conclusion, our investigation is a detailed and systematic report of whole genome characterization of the chitinase family in soybean.
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Affiliation(s)
- Peiyun Lv
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunting Zhang
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Ping Xie
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinyu Yang
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Mohamed A. El-Sheikh
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Daniel Ingo Hefft
- School of Chemical Engineering, Edgbaston Campus, University of Birmingham, Birmingham B15 2TT, UK
| | - Parvaiz Ahmad
- Department of Botany, GDC, Pulwama 192301, Jammu and Kashmir, India
- Correspondence: (P.A.); (T.Z.); (J.A.B.)
| | - Tuanjie Zhao
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (P.A.); (T.Z.); (J.A.B.)
| | - Javaid Akhter Bhat
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (P.A.); (T.Z.); (J.A.B.)
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Crystal structure of the phosphorylated Arabidopsis MKK5 reveals activation mechanism of MAPK kinases. Acta Biochim Biophys Sin (Shanghai) 2022; 54:1159-1170. [PMID: 35866601 PMCID: PMC9909325 DOI: 10.3724/abbs.2022089] [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] [Indexed: 11/25/2022] Open
Abstract
The mitogen-activated protein kinase (MAPK) signaling pathways are highly conserved in eukaryotes, regulating various cellular processes. The MAPK kinases (MKKs) are dual specificity kinases, serving as convergence and divergence points of the tripartite MAPK cascades. Here, we investigate the biochemical characteristics and three-dimensional structure of MKK5 in Arabidopsis (AtMKK5). The recombinant full-length AtMKK5 is phosphorylated and can activate its physiological substrate AtMPK6. There is a conserved kinase interacting motif (KIM) at the N-terminus of AtMKK5, indispensable for specific recognition of AtMPK6. The kinase domain of AtMKK5 adopts active conformation, of which the extended activation segment is stabilized by the phosphorylated Ser221 and Thr215 residues. In line with sequence divergence from other MKKs, the αD and αK helices are missing in AtMKK5, suggesting that the AtMKK5 may adopt distinct modes of upstream kinase/substrate binding. Our data shed lights on the molecular mechanisms of MKK activation and substrate recognition, which may help design specific inhibitors targeting human and plant MKKs.
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Jiang M, Wen G, Zhao C. Phylogeny and evolution of plant Phytochrome Interacting Factors (PIFs) gene family and functional analyses of PIFs in Brachypodium distachyon. PLANT CELL REPORTS 2022; 41:1209-1227. [PMID: 35218399 DOI: 10.1007/s00299-022-02850-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Plant PIFs have been characterized, WGDs contributed to the expansion of class II PIFs; BdPIFs localized in the nucleus; BdPIF4/5C most likely response to high temperature and light stress. Phytochrome interacting factors (PIFs) belong to a small subset of basic helix-loop-helix (bHLH) transcription factors (TFs). As cellular signaling hubs, PIFs integrate multiple external and internal signals to orchestrate the regulation of the transcriptional network, thereby actuating the pleiotropic aspects of downstream morphogenesis. Nevertheless, the origin, phylogeny and function of plant PIFs are not well understood. To elucidate their evolution history and biological function, the comprehensive genomic analysis of the PIF genes was conducted using 40 land plant genomes plus additionally four alga lineages and also performed their gene organizations, sequence features and expression patterns in different subfamilies. In this study, phylogenetic analysis displayed that 246 PIF gene members retrieved from all embryophytes could be divided into three main clades, which were further felled into five distinct classes (Class I-V). The duplications of Class II PIFs were associated specially with whole genome duplication (WGD) events during the plant evolution process. Sequence analysis showed that PIF proteins had a conserved APB motif, and its crucial amino acid residues were relatively high proportion in the average abundance. As expected, subcellular localization analysis revealed that all BdPIF proteins were localized to the nucleus. Especially, BdPIF4/5C showed the highest expression level at high temperature, and the most significant hypocotyl elongation phenotype of overexpression of BdPIFs in Arabidopsis, which was consistent with the function and phenotype of AtPIF4. In brief, our findings provide a novel perspective on the origin and evolutionary history of plant PIFs, and lays a foundation for further investigation on its functions in plant growth and development.
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Affiliation(s)
- Min Jiang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Eco-Chongming (IEC), School of Life Sciences, Fudan University, Shanghai, 200438, China.
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences (CAS), Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
| | - Guosong Wen
- Research and Development Center for Heath Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Changling Zhao
- Research and Development Center for Heath Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
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7
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Jiang M, Li S, Zhao C, Zhao M, Xu S, Wen G. Identification and analysis of sucrose synthase gene family associated with polysaccharide biosynthesis in Dendrobium catenatum by transcriptomic analysis. PeerJ 2022; 10:e13222. [PMID: 35402092 PMCID: PMC8992646 DOI: 10.7717/peerj.13222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/14/2022] [Indexed: 01/12/2023] Open
Abstract
Background Dendrobium catenatum is a valuable traditional medicinal herb with high commercial value. D. catenatum stems contain abundant polysaccharides which are one of the main bioactive components. However, although some genes related to the synthesis of the polysaccharides have been reported, more key genes need to be further elucidated. Results In this study, the contents of polysaccharides and mannose in D. catenatum stems at four developmental stages were compared, and the stems' transcriptomes were analyzed to explore the synthesis mechanism of the polysaccharides. Many genes involved in starch and sucrose metabolisms were identified by KEGG pathway analysis. Further analysis found that sucrose synthase (SUS; EC 2.4.1.13) gene maybe participated in the polysaccharide synthesis. Hence, we further investigated the genomic characteristics and evolution relationships of the SUS family in plants. The result suggested that the SUS gene of D. catenatum (DcSUS) had undergone the expansion characterized by tandem duplication which might be related to the enrichment of the polysaccharides in D. catenatum stems. Moreover, expression analyses of the DcSUS displayed significant divergent patterns in different tissues and could be divided into two main groups in the stems with four developmental stages. Conclusion In general, our results revealed that DcSUS is likely involved in the metabolic process of the stem polysaccharides, providing crucial clues for exploiting the key genes associated with the polysaccharide synthesis.
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Affiliation(s)
- Min Jiang
- Research & Development Center for Heath Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China,Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Eco-Chongming (IEC), School of Life Sciences, Fudan University, Shanghai, China
| | - Shangyun Li
- Research & Development Center for Heath Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Changling Zhao
- Research & Development Center for Heath Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Mingfu Zhao
- Research & Development Center for Heath Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Shaozhong Xu
- Research & Development Center for Heath Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Guosong Wen
- Research & Development Center for Heath Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
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Mitogen-Activated Protein Kinase and Substrate Identification in Plant Growth and Development. Int J Mol Sci 2022; 23:ijms23052744. [PMID: 35269886 PMCID: PMC8911294 DOI: 10.3390/ijms23052744] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/17/2022] [Accepted: 02/28/2022] [Indexed: 02/01/2023] Open
Abstract
Mitogen-activated protein kinases (MAPKs) form tightly controlled signaling cascades that play essential roles in plant growth, development, and defense response. However, the molecular mechanisms underlying MAPK cascades are still very elusive, largely because of our poor understanding of how they relay the signals. The MAPK cascade is composed of MAPK, MAPKK, and MAPKKK. They transfer signals through the phosphorylation of MAPKKK, MAPKK, and MAPK in turn. MAPKs are organized into a complex network for efficient transmission of specific stimuli. This review summarizes the research progress in recent years on the classification and functions of MAPK cascades under various conditions in plants, especially the research status and general methods available for identifying MAPK substrates, and provides suggestions for future research directions.
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Li N, Jiang M, Li P, Li X. Identification, expression, and functional analysis of Hsf and Hsp20 gene families in Brachypodium distachyon under heat stress. PeerJ 2021; 9:e12267. [PMID: 34703676 PMCID: PMC8489411 DOI: 10.7717/peerj.12267] [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: 04/26/2021] [Accepted: 09/16/2021] [Indexed: 12/15/2022] Open
Abstract
Background The heat shock factor (Hsf) and small heat shock protein (sHsp, also called Hsp20) complex has been identified as a primary component in the protection of plant cells from ubiquitous stresses, particularly heat stress. Our study aimed to characterize and analyze the Hsf and Hsp genes in Brachypodium distachyon, an annual temperate grass and model plant in cereal and grass studies. Results We identified 24 Hsf and 18 Hsp20 genes in B. distachyon and explored their evolution in gene organization, sequence features, chromosomal localization, and gene duplication. Our phylogenetic analysis showed that BdHsfs could be divided into three categories and BdHsp20s into ten subfamilies. Further analysis showed that the 3’UTR length of BdHsp20 genes had a negative relationship with their expression under heat stress. Expression analyses indicated that BdHsp20s and BdHsfs were strongly and rapidly induced by high-temperature treatment. Additionally, we constructed a complex regulatory network based on their expression patterns under heat stress. Morphological analysis suggested that the overexpression of five BdHsp20 genes enhanced the seed germination rate and decreased cell death under high temperatures. Conclusion Ultimately, our study provided important evolutionary and functional characterizations for future research on the regulatory mechanisms of BdHsp20s and BdHsfs in herbaceous plants under environmental stress.
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Affiliation(s)
- Na Li
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China.,College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Min Jiang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China.,Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Eco-Chongming (IEC), School of Life Sciences, Fudan University, Shanghai, China
| | - Peng Li
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Xiwen Li
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China.,College of Life Sciences, Shanghai Normal University, Shanghai, China
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González-Coronel JM, Rodríguez-Alonso G, Guevara-García ÁA. A phylogenetic study of the members of the MAPK and MEK families across Viridiplantae. PLoS One 2021; 16:e0250584. [PMID: 33891654 PMCID: PMC8064577 DOI: 10.1371/journal.pone.0250584] [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: 01/04/2021] [Accepted: 04/09/2021] [Indexed: 11/18/2022] Open
Abstract
Protein phosphorylation is regulated by the activity of enzymes generically known as kinases. One of those kinases is Mitogen-Activated Protein Kinases (MAPK), which operate through a phosphorylation cascade conformed by members from three related protein kinase families namely MAPK kinase kinase (MEKK), MAPK kinase (MEK), and MAPK; these three acts hierarchically. Establishing the evolution of these proteins in the plant kingdom is an interesting but complicated task because the current MAPK, MAPKK, and MAPKKK subfamilies arose from duplications and subsequent sub-functionalization during the early stage of the emergence of Viridiplantae. Here, an in silico genomic analysis was performed on 18 different plant species, which resulted in the identification of 96 genes not previously annotated as components of the MAPK (70) and MEK (26) families. Interestingly, a deeper analysis of the sequences encoded by such genes revealed the existence of putative domains not previously described as signatures of MAPK and MEK kinases. Additionally, our analysis also suggests the presence of conserved activation motifs besides the canonical TEY and TDY domains, which characterize the MAPK family.
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Affiliation(s)
- José Manuel González-Coronel
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Gustavo Rodríguez-Alonso
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Ángel Arturo Guevara-García
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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Jiang M, Li P, Wang W. Comparative analysis of MAPK and MKK gene families reveals differential evolutionary patterns in Brachypodium distachyon inbred lines. PeerJ 2021; 9:e11238. [PMID: 33868831 PMCID: PMC8034371 DOI: 10.7717/peerj.11238] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 03/17/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Mitogen-activated protein kinase (MAPK) cascades are involved with signal transduction in almost every aspect of plant growth and development, as well as biotic and abiotic stress responses. The evolutionary analysis of MAPKs and MKKs in individual or entire plant species has been reported, but the evolutionary patterns in the diverse inbred lines of Brachypodium distachyon are still unclear. RESULTS We conducted the systematical molecular evolutionary analysis of B. distachyon. A total of 799 MAPKs and 618 MKKs were identified from 53 B. distachyon inbred lines. Remarkably, only three inbred lines had 16 MPKs and most of those inbred lines lacked MPK7-2 members, whereas 12 MKKs existed in almost all B. distachyon inbred lines. Phylogenetic analysis indicated that MAPKs and MKKs were divided into four groups as previously reported, grouping them in the same branch as corresponding members. MPK21-2 was the exception and fell into two groups, which may be due to their exon-intron patterns, especially the untranslated regions (UTRs). We also found that differential evolution patterns of MKK10 paralogues from ancient tandem duplicates may have undergone functional divergence. Expression analyses suggested that MAPKs and MKKs likely played different roles in different genetic contexts within various tissues and with abiotic stresses. CONCLUSION Our study revealed that UTRs affected the structure and evolution of MPK21-2 genes and the differential evolution of MKK10 paralogues with ancient tandem duplication might have functional divergences. Our findings provide new insights into the functional evolution of genes in closely inbred lines.
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Affiliation(s)
- Min Jiang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai Chenshan Botanical Garden, Shanghai, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Peng Li
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Wei Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), Shanghai Chenshan Botanical Garden, Shanghai, China
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Reprogramming plant specialized metabolism by manipulating protein kinases. ABIOTECH 2021; 2:226-239. [PMID: 34377580 PMCID: PMC8209778 DOI: 10.1007/s42994-021-00053-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/05/2021] [Indexed: 02/08/2023]
Abstract
Being sessile, plants have evolved sophisticated mechanisms to balance between growth and defense to survive in the harsh environment. The transition from growth to defense is commonly achieved by factors, such as protein kinases (PKs) and transcription factors, that initiate signal transduction and regulate specialized metabolism. Plants produce an array of lineage-specific specialized metabolites for chemical defense and stress tolerance. Some of these molecules are also used by humans as drugs. However, many of these defense-responsive metabolites are toxic to plant cells and inhibitory to growth and development. Plants have, thus, evolved complex regulatory networks to balance the accumulation of the toxic metabolites. Perception of external stimuli is a vital part of the regulatory network. Protein kinase-mediated signaling activates a series of defense responses by phosphorylating the target proteins and translating the stimulus into downstream cellular signaling. As biosynthesis of specialized metabolites is triggered when plants perceive stimuli, a possible connection between PKs and specialized metabolism is well recognized. However, the roles of PKs in plant specialized metabolism have not received much attention until recently. Here, we summarize the recent advances in understanding PKs in plant specialized metabolism. We aim to highlight how the stimulatory signals are transduced, leading to the biosynthesis of corresponding metabolites. We discuss the post-translational regulation of specialized metabolism and provide insights into the mechanisms by which plants respond to the external signals. In addition, we propose possible strategies to increase the production of plant specialized metabolites in biotechnological applications using PKs.
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13
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Gallic acid: Pharmacological activities and molecular mechanisms involved in inflammation-related diseases. Biomed Pharmacother 2021; 133:110985. [DOI: 10.1016/j.biopha.2020.110985] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/01/2020] [Accepted: 11/03/2020] [Indexed: 12/12/2022] Open
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Xie Y, Ding M, Zhang B, Yang J, Pei T, Ma P, Dong J. Genome-wide characterization and expression profiling of MAPK cascade genes in Salvia miltiorrhiza reveals the function of SmMAPK3 and SmMAPK1 in secondary metabolism. BMC Genomics 2020; 21:630. [PMID: 32928101 PMCID: PMC7488990 DOI: 10.1186/s12864-020-07023-w] [Citation(s) in RCA: 4] [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: 04/20/2020] [Accepted: 08/25/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The contribution of mitogen-activated protein kinase (MAPK) cascades to plant growth and development has been widely studied, but this knowledge has not yet been extended to the medicinal plant Salvia miltiorrhiza, which produces a number of pharmacologically active secondary metabolites. RESULTS In this study, we performed a genome-wide survey and identified six MAPKKK kinases (MAPKKKKs), 83 MAPKK kinases (MAPKKKs), nine MAPK kinases (MAPKKs) and 18 MAPKs in the S. miltiorrhiza genome. Within each class of genes, a small number of subfamilies were recognized. A transcriptional analysis revealed differences in the genes' behaviour with respect to both their site of transcription and their inducibility by elicitors and phytohormones. Two genes were identified as strong candidates for playing roles in phytohormone signalling. A gene-to-metabolite network was constructed based on correlation analysis, highlighting the likely involvement of two of the cascades in the synthesis of two key groups of pharmacologically active secondary metabolites: phenolic acids and tanshinones. CONCLUSION The data provide insight into the functional diversification and conservation of MAPK cascades in S. miltiorrhiza.
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Affiliation(s)
- Yongfeng Xie
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Meiling Ding
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Bin Zhang
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Jie Yang
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Tianlin Pei
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Pengda Ma
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Juane Dong
- College of Life Sciences, Northwest A&F University, Yangling, China
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15
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Ma J, Jiang X, Yarui A, Danli J, Xiaodie Y, Zhang J, Xu A. Ultraviolet light activates PMK-1/p38 MAPK signaling via MOM-4 and JKK-1 in Caenorhabditis elegans. Toxicol Res (Camb) 2020; 9:461-466. [PMID: 32905206 DOI: 10.1093/toxres/tfaa041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 11/12/2022] Open
Abstract
P38 mitogen-activated protein kinase (p38 MAPK) plays an important role in innate immunity and is activated by ultraviolet (UV) radiation. However, the molecular mechanism underlying UV stress remains unclear. In this study, we reported that UV activated PMK-1/p38 MAPK signaling via JKK-1 and MOM-4 in Caenorhabditis elegans. In C. elegans, different UV radiation doses resulted in PMK-1 phosphorylation. However, pmk-1 mutants failed to demonstrate an altered survival time in response to UV when compared with wild-type worms. Further analysis showed that JKK-1, but not SEK-1 mutants, displayed impaired PMK-1 activation following UV irradiation, suggesting that JKK-1 is the upstream MAP2K for the activation of PMK-1 in C. elegans under UV stimulation. UV-induced activation of PMK-1 was markedly reduced in MOM-4, but not in NSY-1 and DLK-1 mutant worms, suggesting that MOM-4 is the upstream MAP3K regulator of PMK-1 activation in response to UV stress in C. elegans. Additionally, daf-16 mutants displayed a shorter lifespan under UV stress, but UV-induced activation of PMK-1 was not markedly reduced in daf-16 and age-1 mutant worms. Our results revealed the signaling pathway involved in PMK-1 activation in C. elegans in response to UV radiation.
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Affiliation(s)
- Jing Ma
- Department of Pharmacy, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, 1665 Kongjiang Road, Shanghai 200092, China
| | - Xinghao Jiang
- School of Information Security Engineering, Shanghai JiaoTong University, 800 Jianchuan Road, Shanghai 200240, China
| | - An Yarui
- College of Science, University of Shanghai for Science and Technology, 1100 Jungong Road, Shanghai 200093, China
| | - Jin Danli
- College of Science, University of Shanghai for Science and Technology, 1100 Jungong Road, Shanghai 200093, China
| | - Yin Xiaodie
- College of Science, University of Shanghai for Science and Technology, 1100 Jungong Road, Shanghai 200093, China
| | - Jian Zhang
- Department of Pharmacy, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, 1665 Kongjiang Road, Shanghai 200092, China
| | - Ajing Xu
- Department of Pharmacy, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, 1665 Kongjiang Road, Shanghai 200092, China
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Martinez SA, Shorinola O, Conselman S, See D, Skinner DZ, Uauy C, Steber CM. Exome sequencing of bulked segregants identified a novel TaMKK3-A allele linked to the wheat ERA8 ABA-hypersensitive germination phenotype. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:719-736. [PMID: 31993676 PMCID: PMC7021667 DOI: 10.1007/s00122-019-03503-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/06/2019] [Indexed: 05/09/2023]
Abstract
Using bulked segregant analysis of exome sequence, we fine-mapped the ABA-hypersensitive mutant ERA8 in a wheat backcross population to the TaMKK3-A locus of chromosome 4A. Preharvest sprouting (PHS) is the germination of mature grain on the mother plant when it rains before harvest. The ENHANCED RESPONSE TO ABA8 (ERA8) mutant increases seed dormancy and, consequently, PHS tolerance in soft white wheat 'Zak.' ERA8 was mapped to chromosome 4A in a Zak/'ZakERA8' backcross population using bulked segregant analysis of exome sequenced DNA (BSA-exome-seq). ERA8 was fine-mapped relative to mutagen-induced SNPs to a 4.6 Mb region containing 70 genes. In the backcross population, the ERA8 ABA-hypersensitive phenotype was strongly linked to a missense mutation in TaMKK3-A-G1093A (LOD 16.5), a gene associated with natural PHS tolerance in barley and wheat. The map position of ERA8 was confirmed in an 'Otis'/ZakERA8 but not in a 'Louise'/ZakERA8 mapping population. This is likely because Otis carries the same natural PHS susceptible MKK3-A-A660S allele as Zak, whereas Louise carries the PHS-tolerant MKK3-A-C660R allele. Thus, the variation for grain dormancy and PHS tolerance in the Louise/ZakERA8 population likely resulted from segregation of other loci rather than segregation for PHS tolerance at the MKK3 locus. This inadvertent complementation test suggests that the MKK3-A-G1093A mutation causes the ERA8 phenotype. Moreover, MKK3 was a known ABA signaling gene in the 70-gene 4.6 Mb ERA8 interval. None of these 70 genes showed the differential regulation in wild-type Zak versus ERA8 expected of a promoter mutation. Thus, the working model is that the ERA8 phenotype results from the MKK3-A-G1093A mutation.
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Affiliation(s)
- Shantel A Martinez
- Molecular Plant Sciences, Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
| | | | - Samantha Conselman
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
| | - Deven See
- Molecular Plant Sciences, Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
- USDA-ARS Wheat Genetics, Quality, Physiology and Disease Research Unit, Washington State University, Pullman, WA, 99164-6420, USA
| | - Daniel Z Skinner
- Molecular Plant Sciences, Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
- USDA-ARS Wheat Genetics, Quality, Physiology and Disease Research Unit, Washington State University, Pullman, WA, 99164-6420, USA
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Camille M Steber
- Molecular Plant Sciences, Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA.
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA.
- USDA-ARS Wheat Genetics, Quality, Physiology and Disease Research Unit, Washington State University, Pullman, WA, 99164-6420, USA.
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Tang Z, Cao X, Zhang Y, Jiang J, Qiao D, Xu H, Cao Y. Two splice variants of the DsMEK1 mitogen-activated protein kinase kinase (MAPKK) are involved in salt stress regulation in Dunaliella salina in different ways. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:147. [PMID: 32843896 PMCID: PMC7439689 DOI: 10.1186/s13068-020-01786-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 04/24/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Dunaliella salina can produce glycerol under salt stress, and this production can quickly adapt to changes in external salt concentration. Notably, glycerol is an ideal energy source. In recent years, it has been reported that the mitogen-activated protein kinase cascade pathway plays an important role in regulating salt stress, and in Dunaliella tertiolecta DtMAPK can regulate glycerol synthesis under salt stress. Therefore, it is highly important to study the relationship between the MAPK cascade pathway and salt stress in D. salina and modify it to increase the production of glycerol. RESULTS In our study, we identified and analysed the alternative splicing of DsMEK1 (DsMEK1-X1, DsMEK1-X2) from the unicellular green alga D. salina. DsMEK1-X1 and DsMEK1-X2 were both localized in the cytoplasm. qRT-PCR assays showed that DsMEK1-X2 was induced by salt stress. Overexpression of DsMEK1-X2 revealed a higher increase rate of glycerol production compared to the control and DsMEK1-X1-oe under salt stress. Under salt stress, the expression of DsGPDH2/3/5/6 increased in DsMEK1-X2-oe strains compared to the control. This finding indicated that DsMEK1-X2 was involved in the regulation of DsGPDH expression and glycerol overexpression under salt stress. Overexpression of DsMEK1-X1 increased the proline content and reduced the MDA content under salt stress, and DsMEK1-X1 was able to regulate oxidative stress; thus, we hypothesized that DsMEK1-X1 could reduce oxidative damage under salt stress. Yeast two-hybrid analysis showed that DsMEK1-X2 could interact with DsMAPKKK1/2/3/9/10/17 and DsMAPK1; however, DsMEK1-X1 interacted with neither upstream MAPKKK nor downstream MAPK. DsMEK1-X2-oe transgenic lines increased the expression of DsMAPKKK1/3/10/17 and DsMAPK1, and DsMEK1-X2-RNAi lines decreased the expression of DsMAPKKK2/10/17. DsMEK1-X1-oe transgenic lines did not exhibit increased gene expression, except for DsMAPKKK9. CONCLUSION Our findings demonstrate that DsMEK1-X1 and DsMEK1-X2 can respond to salt stress by two different pathways. The DsMEK1-X1 response to salt stress reduces oxidative damage; however, the DsMAPKKK1/2/3/9/10/17-DsMEK1-X2-DsMAPK1 cascade is involved in the regulation of DsGPDH expression and thus glycerol synthesis under salt stress.
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Affiliation(s)
- Ziyi Tang
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065 China
| | - Xiyue Cao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065 China
| | - Yiping Zhang
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065 China
| | - Jia Jiang
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065 China
| | - Dairong Qiao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065 China
| | - Hui Xu
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065 China
| | - Yi Cao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065 China
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18
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Niu C, Jiang M, Li N, Cao J, Hou M, Ni DA, Chu Z. Integrated bioinformatics analysis of As, Au, Cd, Pb and Cu heavy metal responsive marker genes through Arabidopsis thaliana GEO datasets. PeerJ 2019; 7:e6495. [PMID: 30918749 PMCID: PMC6428040 DOI: 10.7717/peerj.6495] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 01/19/2019] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Current environmental pollution factors, particularly the distribution and diffusion of heavy metals in soil and water, are a high risk to local environments and humans. Despite striking advances in methods to detect contaminants by a variety of chemical and physical solutions, these methods have inherent limitations such as small dimensions and very low coverage. Therefore, identifying novel contaminant biomarkers are urgently needed. METHODS To better track heavy metal contaminations in soil and water, integrated bioinformatics analysis to identify biomarkers of relevant heavy metal, such as As, Cd, Pb and Cu, is a suitable method for long-term and large-scale surveys of such heavy metal pollutants. Subsequently, the accuracy and stability of the results screened were experimentally validated by quantitative PCR experiment. RESULTS We obtained 168 differentially expressed genes (DEGs) which contained 59 up-regulated genes and 109 down-regulated genes through comparative bioinformatics analyses. Subsequently, the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichments of these DEGs were performed, respectively. GO analyses found that these DEGs were mainly related to responses to chemicals, responses to stimulus, responses to stress, responses to abiotic stimulus, and so on. KEGG pathway analyses of DEGs were mainly involved in the protein degradation process and other biologic process, such as the phenylpropanoid biosynthesis pathways and nitrogen metabolism. Moreover, we also speculated that nine candidate core biomarker genes (namely, NILR1, PGPS1, WRKY33, BCS1, AR781, CYP81D8, NR1, EAP1 and MYB15) might be tightly correlated with the response or transport of heavy metals. Finally, experimental results displayed that these genes had the same expression trend response to different stresses as mentioned above (Cd, Pb and Cu) and no mentioned above (Zn and Cr). CONCLUSION In general, the identified biomarker genes could help us understand the potential molecular mechanisms or signaling pathways responsive to heavy metal stress in plants, and could be applied as marker genes to track heavy metal pollution in soil and water through detecting their expression in plants growing in those environments.
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Affiliation(s)
- Chao Niu
- School of Ecological Technology and Engineering, Shanghai Institute of Technology, Shanghai, Shanghai, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, Shanghai, China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, Shanghai, China
| | - Min Jiang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, Shanghai, China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, Shanghai, China
| | - Na Li
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, Shanghai, China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, Shanghai, China
- College of Life Sciences, Shanghai Normal University, Shanghai, Shanghai, China
| | - Jianguo Cao
- College of Life Sciences, Shanghai Normal University, Shanghai, Shanghai, China
| | - Meifang Hou
- School of Ecological Technology and Engineering, Shanghai Institute of Technology, Shanghai, Shanghai, China
| | - Di-an Ni
- School of Ecological Technology and Engineering, Shanghai Institute of Technology, Shanghai, Shanghai, China
| | - Zhaoqing Chu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, Shanghai, China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, Shanghai, China
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Wang C, Wang Y, Pan Q, Chen S, Feng C, Hai J, Li H. Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide. BMC Genomics 2019; 20:142. [PMID: 30770726 PMCID: PMC6377786 DOI: 10.1186/s12864-019-5494-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/29/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Plant Trihelix transcription factors, specifically bind to GT elements and play important roles in plant physiology and development. Wheat is a main cereal crop. Brachypodium distachyon is a close relative of wheat and has been described as a new model species for studying of grass functional genomics. Presently, little is known about wheat and B. distachyon Trihelix genes. RESULTS In 51 species, 2387 Trihelix genes were identified, including 80 wheat Trihelix genes and 27 B. distachyon Trihelix genes. Consistent with the results of previous studies, these genes were classified into five subfamilies: GT-1, GT-2, SIP1, GTγ, and SH4. Members of the same subfamily shared similar gene structures and common motifs. Most TaGT and BdGT genes contained many kinds of cis-elements, such as development-, stress-, and phytohormone-related cis-acting elements. Additionally, 21 randomly selected TaGT genes were mainly expressed in the roots and flowers, while the expression of 19 selected BdGT genes was constitutive. These results indicate that the roles of Trihelix genes in wheat and B. distachyon might have diversified during the evolutionary process. The expression of the most selected TaGT and BdGT genes was down-regulated when exposed to low temperatures, NaCl, ABA, and PEG, implying that TaGT and BdGT genes negatively respond to abiotic stress. On the contrary, the expression of some genes was up-regulated under heat stress. CONCLUSIONS Trihelix genes exist extensively in plants and have many functions. During the evolutionary process, this gene family expanded and their functions diversified. As a result, the expression pattern and functions of members of the same family might be different. This study lays a foundation for further functional analyses of TaGT and BdGT genes.
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Affiliation(s)
- Chengwei Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712000 China
| | - Yu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712000 China
| | - Qi Pan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712000 China
| | - Shoukun Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712000 China
| | - Cuizhu Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712000 China
| | - Jiangbo Hai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712000 China
| | - Haifeng Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712000 China
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In silico-prediction of protein-protein interactions network about MAPKs and PP2Cs reveals a novel docking site variants in Brachypodium distachyon. Sci Rep 2018; 8:15083. [PMID: 30305661 PMCID: PMC6180098 DOI: 10.1038/s41598-018-33428-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 09/13/2018] [Indexed: 12/26/2022] Open
Abstract
Protein-protein interactions (PPIs) underlie the molecular mechanisms of most biological processes. Mitogen-activated protein kinases (MAPKs) can be dephosphorylated by MAPK-specific phosphatases such as PP2C, which are critical to transduce extracellular signals into adaptive and programmed responses. However, the experimental approaches for identifying PPIs are expensive, time-consuming, laborious and challenging. In response, many computational methods have been developed to predict PPIs. Yet, these methods have inherent disadvantages such as high false positive and negative results. Thus, it is crucial to develop in silico approaches for predicting PPIs efficiently and accurately. In this study, we identified PPIs among 16 BdMAPKs and 86 BdPP2Cs in B. distachyon using a novel docking approach. Further, we systematically investigated the docking site (D-site) of BdPP2C which plays a vital role for recognition and docking of BdMAPKs. D-site analysis revealed that there were 96 pairs of PPIs including all BdMAPKs and most BdPP2Cs, which indicated that BdPP2C may play roles in other signaling networks. Moreover, most BdPP2Cs have a D-site for BdMAPKs in our prediction results, which suggested that our method can effectively predict PPIs, as confirmed by their 3D structure. In addition, we validated this methodology with known Arabidopsis and yeast phosphatase-MAPK interactions from the STRING database. The results obtained provide a vital research resource for exploring an accurate network of PPIs between BdMAPKs and BdPP2Cs.
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