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Wu T, Yang Q, Zhou R, Yu T, Shen S, Cao R, Ma X, Song X. Large-scale analysis of trihelix transcription factors reveals their expansion and evolutionary footprint in plants. PHYSIOLOGIA PLANTARUM 2023; 175:e14039. [PMID: 37882297 DOI: 10.1111/ppl.14039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 09/11/2023] [Accepted: 09/25/2023] [Indexed: 10/27/2023]
Abstract
The trihelix transcription factor (TTF) gene family is an important class of transcription factors that play key roles in regulating developmental processes and responding to various stresses. To date, no comprehensive analysis of the TTF gene family in large-scale species has been performed. A cross-genome exploration of its origin, copy number variation, and expression pattern in plants is also unavailable. Here, we identified and characterized the TTF gene family in 110 species representing typical plant phylogenetic taxa. Interestingly, we found that the number of TTF genes was significantly expanded in Chara braunii compared to other species. Based on the available plant genomic datasets, our comparative analysis suggested that the TTF gene family likely originated from the GT-1-1 group and then expanded to form other groups through duplication or deletion of some domains. We found evidence that whole-genome duplication/triplication contributed most to the expansion of the TTF gene family in dicots, monocots and basal angiosperms. In contrast, dispersed and proximal duplications contributed to the expansion of the TTF gene family in algae and bryophyta. The expression patterns of TTF genes and their upstream and downstream genes in different treatments showed a functional divergence of TTF-related genes. Furthermore, we constructed the interaction network between TTF genes and the corresponding upstream and downstream genes, providing a blueprint for their regulatory pathways. This study provided a cross-genome comparative analysis of TTF genes in 110 species, which contributed to understanding their copy number expansion and evolutionary footprint in plants.
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Affiliation(s)
- Tong Wu
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, China
| | - Qihang Yang
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, China
| | - Rong Zhou
- Department of Food Science, Aarhus University, Aarhus, Denmark
| | - Tong Yu
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, China
| | - Shaoqin Shen
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, China
| | - Rui Cao
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, China
| | - Xiao Ma
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, China
- College of Horticultural Science & Technology, Hebei Normal University Of Science & Technology, Qinhuangdao, Hebei, China
| | - Xiaoming Song
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, China
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Hu J, Liu T, Huo H, Liu S, Liu M, Liu C, Zhao M, Wang K, Wang Y, Zhang M. Genome-wide characterization, evolutionary analysis, and expression pattern analysis of the trihelix transcription factor family and gene expression analysis under MeJA treatment in Panax ginseng. BMC PLANT BIOLOGY 2023; 23:376. [PMID: 37525122 PMCID: PMC10392005 DOI: 10.1186/s12870-023-04390-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 07/22/2023] [Indexed: 08/02/2023]
Abstract
Panax ginseng is a well-known medicinal plant with several pharmacological uses in China. The trihelix family transcription factors, also known as GT factors, can be involved in the regulation of growth and developmental processes in plants. There have been no in-depth reports or systematic studies about the trihelix transcription factor in ginseng. In this study, the structure, chromosomal localization, gene duplication, phylogeny, functional differentiation, expression patterns and coexpression interactions of trihelix transcripts were analysed using bioinformatics methods based on the ginseng transcriptome database. Thirty-two trihelix transcription factor genes were identified in ginseng, and these genes were alternatively spliced to obtain 218 transcripts. These transcripts were unevenly distributed on different chromosomes of ginseng, and phylogenetic analysis classified the PgGT transcripts into five subgroups. Gene Ontology (GO) analysis classified PgGT transcripts into eight functional subclasses, indicating that they are functionally diverse. The expression pattern analysis of 218 PgGT transcripts revealed that their expression was tissue-specific and spatiotemporally-specific in 14 different tissues of 4-year-old ginseng, 4 different ages of ginseng roots, and 42 farmers' cultivars of 4-year-old ginseng roots. Despite the differences in the expression patterns of these transcripts, coexpression network analysis revealed that these transcripts could be expressed synergistically in ginseng. In addition, two randomly selected PgGT transcripts in each of the five different subfamilies were subjected to methyl jasmonate treatment at different times, and PgGT was able to respond to the regulation of methy1 jasmonate. These results provide a theoretical basis and gene resources for an in-depth study of the function of trihelix genes in other plants.
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Affiliation(s)
- Jian Hu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China
| | - Tao Liu
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China
| | - Huimin Huo
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China
| | - Sizhang Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China
| | - Mingming Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China
| | - Chang Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China
| | - Mingzhu Zhao
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China
| | - Kangyu Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China.
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China.
| | - Yi Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China.
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China.
| | - Meiping Zhang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China.
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun, Jilin, 130118, China.
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Aggarwal PR, Pramitha L, Choudhary P, Singh RK, Shukla P, Prasad M, Muthamilarasan M. Multi-omics intervention in Setaria to dissect climate-resilient traits: Progress and prospects. FRONTIERS IN PLANT SCIENCE 2022; 13:892736. [PMID: 36119586 PMCID: PMC9470963 DOI: 10.3389/fpls.2022.892736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Millets constitute a significant proportion of underutilized grasses and are well known for their climate resilience as well as excellent nutritional profiles. Among millets, foxtail millet (Setaria italica) and its wild relative green foxtail (S. viridis) are collectively regarded as models for studying broad-spectrum traits, including abiotic stress tolerance, C4 photosynthesis, biofuel, and nutritional traits. Since the genome sequence release, the crop has seen an exponential increase in omics studies to dissect agronomic, nutritional, biofuel, and climate-resilience traits. These studies have provided first-hand information on the structure, organization, evolution, and expression of several genes; however, knowledge of the precise roles of such genes and their products remains elusive. Several open-access databases have also been instituted to enable advanced scientific research on these important crops. In this context, the current review enumerates the contemporary trend of research on understanding the climate resilience and other essential traits in Setaria, the knowledge gap, and how the information could be translated for the crop improvement of related millets, biofuel crops, and cereals. Also, the review provides a roadmap for studying other underutilized crop species using Setaria as a model.
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Affiliation(s)
- Pooja Rani Aggarwal
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Lydia Pramitha
- School of Agriculture and Biosciences, Karunya Institute of Technology and Sciences, Coimbatore, Tamil Nadu, India
| | - Pooja Choudhary
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | | | - Pooja Shukla
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Manoj Prasad
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
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Zhu M, Bin J, Ding H, Pan D, Tian Q, Yang X, Wang L, Yue Y. Insights into the trihelix transcription factor responses to salt and other stresses in Osmanthus fragrans. BMC Genomics 2022; 23:334. [PMID: 35488201 PMCID: PMC9055724 DOI: 10.1186/s12864-022-08569-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 04/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Osmanthus fragrans is an evergreen plant with high ornamental and economic values. However, they are easily injured by salt stress, which severely limits their use in high salinity areas. The trihelix transcription factor (TF) family, as one of the earliest discovered TF families in plants, plays an essential part in responses to different abiotic stresses, and it has potential functions in improving the salt-tolerance capability of O. fragrans. RESULTS In this study, 56 trihelix genes (OfGTs) were first identified in O. fragrans and then divided into five subfamilies in accordance with a phylogenetic tree analysis. The OfGTs were found to be located randomly on the 20 O. fragrans chromosomes, and an analysis of gene replication events indicated that the OfGT gene family underwent strong purification selection during the evolutionary process. The analysis of conserved motifs and gene structures implied that the OfGT members in the same subfamily have similar conserved motifs and gene structures. A promoter cis-elements analysis showed that all the OfGT genes contained multiple abiotic and hormonal stress-related cis-elements. The RNA-seq data suggested that the OfGTs have specific expression patterns in different tissues, and some were induced by salt stress. The qRT-PCR analysis of 12 selected OfGTs confirmed that OfGT1/3/21/33/42/45/46/52 were induced, with OfGT3/42/46 being the most highly expressed. In addition, OfGT42/OfGT46 had a co-expression pattern under salt-stress conditions. OfGT3/42/46 were mainly localized in the nuclei and exhibited no transcriptional activities based on the analysis of the subcellular localization and transcriptional activity assay. Furthermore, the expression levels of most of the selected OfGTs were induced by multiple abiotic and hormonal stresses, and the expression patterns of some OfGTs were also highly correlated with gibberellic acid and methyl jasmonate levels. Remarkably, the transient transformation results showed lower MDA content and increased expression of ROS-related genes NbAPX in transgenic plants, which implying OfGT3/42/46 may improve the salt tolerance of tobacco. CONCLUSIONS The results implied that the OfGT genes were related to abiotic and hormonal stress responses in O. fragrans, and that the OfGT3/42/46 genes in particular might play crucial roles in responses to salt stress. This study made a comprehensive summary of the OfGT gene family, including functions and co-expression patterns in response to salt and other stresses, as well as an evolutionary perspective. Consequently, it lays a foundation for further functional characterizations of these genes.
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Affiliation(s)
- Meilin Zhu
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing, 210037, People's Republic of China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, People's Republic of China
| | - Jing Bin
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing, 210037, People's Republic of China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, People's Republic of China
| | - Huifen Ding
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing, 210037, People's Republic of China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, People's Republic of China
| | - Duo Pan
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing, 210037, People's Republic of China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, People's Republic of China
| | - Qingyin Tian
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing, 210037, People's Republic of China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, People's Republic of China
| | - Xiulian Yang
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing, 210037, People's Republic of China.,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, People's Republic of China
| | - Lianggui Wang
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing, 210037, People's Republic of China. .,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, People's Republic of China.
| | - Yuanzheng Yue
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing, 210037, People's Republic of China. .,Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, People's Republic of China.
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Chen H, Ji K, Li Y, Gao Y, Liu F, Cui Y, Liu Y, Ge W, Wang Z. Triplication is the main evolutionary driving force of NLP transcription factor family in Chinese cabbage and related species. Int J Biol Macromol 2022; 201:492-506. [PMID: 35051503 DOI: 10.1016/j.ijbiomac.2022.01.082] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/09/2022] [Accepted: 01/12/2022] [Indexed: 11/25/2022]
Abstract
The NODULE-INCEPTION-like protein (NLP) is a plant-specific transcription factor (TF) family that plays an important role in both signal transduction and nitrate assimilation. However, the NLP gene family in Chinese cabbage (Brassica rapa) has yet to be studied. Here we identified 17, 16, and 32 NLP genes in Chinese cabbage, Brassica oleracea, and Brassica napus, respectively. We found that duplication of those NLP genes almost always originated from genome-wide duplication events. Further analysis (using Arabidopsis as a reference) revealed that the NLP family in Chinese cabbage and B. oleracea was characterized by direct expansion caused by whole-genome duplication. By contrast, indirect expansion characterized B. napus, which arose from hybridization and fusion of the two species. In addition, phylogenetic and homology analyses showed that the Brassica NLP gene family has been highly conserved in evolution. Finally, we also identified optimal codons for four studied species. Altogether, through comparative genome analysis methods, we presented compelling evidence that triplication is the main driving force for the NLP TF family's evolution in Chinese cabbage and related Brassica plants, a process evidently highly conserved. This work will help in better understanding the impact of genome-wide duplication on gene families of plants.
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Affiliation(s)
- Huilong Chen
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China; School of Information Science and Technology, Yanching Institute of Technology, Langfang, Hebei 065000, China
| | - Kexin Ji
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Yuxian Li
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Yaliu Gao
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Fang Liu
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Yutong Cui
- College of Management, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Ying Liu
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Weina Ge
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China.
| | - Zhenyi Wang
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China.
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Wang T, Hu J, Ma X, Li C, Yang Q, Feng S, Li M, Li N, Song X. Identification, evolution and expression analyses of whole genome-wide TLP gene family in Brassica napus. BMC Genomics 2020; 21:264. [PMID: 32228446 PMCID: PMC7106719 DOI: 10.1186/s12864-020-6678-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 03/13/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Brassica is a very important genus of Brassicaceae, including many important oils, vegetables, forage crops, and ornamental horticultural plants. TLP family genes play important regulatory roles in the growth and development of plants. Therefore, this study used a bioinformatics approach to conduct the systematic comparative genomics analysis of TLP gene family in B. napus and other three important Brassicaceae crops. RESULTS Here, we identified a total of 29 TLP genes from B. napus genome, and they distributed on 16 chromosomes of B. napus. The evolutionary relationship showed that these genes could be divided into six groups from Group A to F. We found that the gene corresponding to Arabidopsis thaliana AT1G43640 was completely lost in B. rapa, B. oleracea and B. napus after whole genome triplication. The gene corresponding to AT1G25280 was retained in all the three species we analysed, belonging to 1:3:6 ratios. Our analyses suggested that there was a selective loss of some genes that might be redundant after genome duplication. This study proposed that the TLP genes in B. napus did not directly expansion compared with its diploid parents B. rapa, and B. oleracea. Instead, an indirect expansion of TLP gene family occurred in its two diploid parents. In addition, the study further utilized RNA-seq to detect the expression pattern of TLP genes between different tissues and two subgenomes. CONCLUSIONS This study systematically conducted the comparative analyses of TLP gene family in B. napus, discussed the loss and expansion of genes after genome duplication. It provided rich gene resources for exploring the molecular mechanism of TLP gene family. Meanwhile, it provided guidance and reference for the research of other gene families in B. napus.
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Affiliation(s)
- Tong Wang
- College of Life Sciences, North China University of Science and Technology, 21 Bohai Road, Caofeidian Xincheng, Tangshan, 063210, Hebei, China
| | - Jingjing Hu
- College of Life Sciences, North China University of Science and Technology, 21 Bohai Road, Caofeidian Xincheng, Tangshan, 063210, Hebei, China
| | - Xiao Ma
- Library, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Chunjin Li
- College of Life Sciences, North China University of Science and Technology, 21 Bohai Road, Caofeidian Xincheng, Tangshan, 063210, Hebei, China
| | - Qihang Yang
- College of Life Sciences, North China University of Science and Technology, 21 Bohai Road, Caofeidian Xincheng, Tangshan, 063210, Hebei, China
| | - Shuyan Feng
- College of Life Sciences, North China University of Science and Technology, 21 Bohai Road, Caofeidian Xincheng, Tangshan, 063210, Hebei, China
| | - Miaomiao Li
- College of Life Sciences, North China University of Science and Technology, 21 Bohai Road, Caofeidian Xincheng, Tangshan, 063210, Hebei, China
| | - Nan Li
- College of Life Sciences, North China University of Science and Technology, 21 Bohai Road, Caofeidian Xincheng, Tangshan, 063210, Hebei, China.
| | - Xiaoming Song
- College of Life Sciences, North China University of Science and Technology, 21 Bohai Road, Caofeidian Xincheng, Tangshan, 063210, Hebei, China.
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Liu W, Zhang Y, Li W, Lin Y, Wang C, Xu R, Zhang L. Genome-wide characterization and expression analysis of soybean trihelix gene family. PeerJ 2020; 8:e8753. [PMID: 32206450 PMCID: PMC7075366 DOI: 10.7717/peerj.8753] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 02/14/2020] [Indexed: 01/10/2023] Open
Abstract
Trihelix transcription factors play multiple roles in plant growth, development and various stress responses. In this study, we identified 71 trihelix family genes in the soybean genome. These trihelix genes were located at 19 out of 20 soybean chromosomes unevenly and were classified into six distinct subfamilies: GT-1, GT-2, GTγ, SIP1, SH4 and GTδ. The gene structure and conserved functional domain of these trihelix genes were similar in the same subfamily but diverged between different subfamilies. Thirteen segmental duplicated gene pairs were identified and all of them experienced a strong purifying selective pressure during evolution. Various stress-responsive cis-elements presented in the promoters of soybean trihelix genes, suggesting that the trihelix genes might respond to the environmental stresses in soybean. The expression analysis suggests that trihelix genes are involved in diverse functions during soybean development, flood or salinity tolerance, and plant immunity. Our results provide genomic information of the soybean trihelix genes and a basis for further characterizing their roles in response to environmental stresses.
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Affiliation(s)
- Wei Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China.,Shandong Engineering Laboratory of Featured Crops, Jinan, China
| | - Yanwei Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China.,Shandong Engineering Laboratory of Featured Crops, Jinan, China
| | - Wei Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China.,Shandong Engineering Laboratory of Featured Crops, Jinan, China
| | - Yanhui Lin
- Institute of Food Crops, Hainan Academy of Agricultural Sciences, Haikou, China
| | - Caijie Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China.,Shandong Engineering Laboratory of Featured Crops, Jinan, China
| | - Ran Xu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China.,Shandong Engineering Laboratory of Featured Crops, Jinan, China
| | - Lifeng Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China.,Shandong Engineering Laboratory of Featured Crops, Jinan, China
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8
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Lan J, Zhang R, Yu H, Wang J, Xue W, Chen J, Lin S, Wang Y, Xie Z, Jiang S. Quantitative Proteomic Analysis Uncovers the Mediation of Endoplasmic Reticulum Stress-Induced Autophagy in DHAV-1-Infected DEF Cells. Int J Mol Sci 2019; 20:ijms20246160. [PMID: 31817666 PMCID: PMC6940786 DOI: 10.3390/ijms20246160] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 12/11/2022] Open
Abstract
Autophagy is a tightly regulated catabolic process and is activated in cells in response to stress signals. Despite extensive study, the interplay between duck hepatitis A virus type 1 (DHAV-1) and the autophagy of host cells is not clear. In this study, we applied proteomics analysis to investigate the interaction mechanism between DHAV-1 and duck embryo fibroblast (DEF) cells. In total, 507 differentially expressed proteins (DEPs) were identified, with 171 upregulated proteins and 336 downregulated proteins. The protein expression level of heat shock proteins (Hsps) and their response to stimulus proteins and zinc finger proteins (ZFPs) were significantly increased while the same aspects of ribosome proteins declined. Bioinformatics analysis indicated that DEPs were mainly involved in the “response to stimulus”, the “defense response to virus”, and the “phagosome pathway”. Furthermore, Western blot results showed that the conversion of microtubule-associated protein 1 light chain 3-I (LC3-I) to the lipidation form of LC3-II increased, and the conversion rate decreased when DEF cells were processed with 4-phenylbutyrate (4-PBA). These findings indicated that DHAV-1 infection could cause endoplasmic reticulum (ER) stress-induced autophagy in DEF cells, and that ER stress was an important regulatory factor in the activation of autophagy. Our data provide a new clue regarding the host cell response to DHAV-1 and identify proteins involved in the DHAV-1 infection process or the ER stress-induced autophagy process.
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Affiliation(s)
- Jingjing Lan
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271000, China; (J.L.); (R.Z.); (H.Y.); (J.W.); (W.X.); (J.C.); (Z.X.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271000, China
| | - Ruihua Zhang
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271000, China; (J.L.); (R.Z.); (H.Y.); (J.W.); (W.X.); (J.C.); (Z.X.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271000, China
| | - Honglei Yu
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271000, China; (J.L.); (R.Z.); (H.Y.); (J.W.); (W.X.); (J.C.); (Z.X.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271000, China
| | - Jingyu Wang
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271000, China; (J.L.); (R.Z.); (H.Y.); (J.W.); (W.X.); (J.C.); (Z.X.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271000, China
| | - Wenxiang Xue
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271000, China; (J.L.); (R.Z.); (H.Y.); (J.W.); (W.X.); (J.C.); (Z.X.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271000, China
| | - Junhao Chen
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271000, China; (J.L.); (R.Z.); (H.Y.); (J.W.); (W.X.); (J.C.); (Z.X.)
- College of Public Health and Management, Weifang Medical University, Weifang 261042, China
| | - Shaoli Lin
- Molecular Virology Laboratory, VA-MD College of Veterinary Medicine and Maryland Pathogen Research Institute, University of Maryland, College Park, MD 20742, USA;
| | - Yu Wang
- Department of Basic Medical Sciences, Taishan Medical College, Taian 271000, China;
| | - Zhijing Xie
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271000, China; (J.L.); (R.Z.); (H.Y.); (J.W.); (W.X.); (J.C.); (Z.X.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271000, China
| | - Shijin Jiang
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271000, China; (J.L.); (R.Z.); (H.Y.); (J.W.); (W.X.); (J.C.); (Z.X.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271000, China
- Correspondence: ; Tel.: +86-538-8245799
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