1
|
Heckmann A, Perochon A, Doohan FM. Genome-wide analysis of salicylic acid and jasmonic acid signalling marker gene families in wheat. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:691-704. [PMID: 38864777 DOI: 10.1111/plb.13659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 03/25/2024] [Indexed: 06/13/2024]
Abstract
Jasmonic acid (JA) and salicylic acid (SA) phytohormone pathways are important regulators of stress tolerance. Knowledge regarding the diversity, phylogeny and functionality of wheat genes involved in JA and SA response is limited. Using Arabidopsis, rice and wheat genomic and wheat disease transcriptomic data, we deduced the size, phylogenetic diversity and pathogen-responsiveness of seven hormone-responsive gene families, and thus selected 14 candidates as potential hormone responsive gene markers. Gene-specific expression studies assessed the impact of exogenous JA and SA on their transcriptional activation in leaves of two distinct wheat cultivars. RNAseq data were interrogated to assess their disease responsiveness and tissue-specific expression. This study elucidated the number, phylogeny and pathogen-responsiveness of wheat genes from seven families, including 12 TaAOS, 6 TaJAMyb, 256 TaWRKY group III, 85 TaPR1, 205 TaPR2, 76 TaPR3 and 124 TaPR5. This included the first description of the wheat AOS, JAMyb, PR2, PR3 and PR5 gene families. Gene expression studies delineated TaAOS1-5B and TaJAMyb-4A as JA-responsive in leaves, but not significantly responsive to SA treatment, while TaWRKY45-B was a SA- but not a JA-responsive marker. Other candidate genes were either unresponsive or non-specific to SA or JA. Our findings highlight that all seven gene families are greatly expanded in wheat as compared to other plants (up to 7.6-fold expansion), and demonstrate disparity in the response to biotic stress between some homoeologous and paralogous sequences within these families. The SA- and JA-responsive marker genes identified herein will prove useful tools to monitor these signalling pathways in wheat.
Collapse
Affiliation(s)
- A Heckmann
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Dublin, Ireland
| | - A Perochon
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Dublin, Ireland
| | - F M Doohan
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Dublin, Ireland
| |
Collapse
|
2
|
Ngaki MN, Srivastava SK, Feifei W, Bhattacharyya MK. The soybean plasma membrane GmDR1 protein conferring broad-spectrum disease and pest resistance regulates several receptor kinases and NLR proteins. Sci Rep 2024; 14:12253. [PMID: 38806545 PMCID: PMC11133457 DOI: 10.1038/s41598-024-62332-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 05/15/2024] [Indexed: 05/30/2024] Open
Abstract
Overexpression of Glycine max disease resistant 1 (GmDR1) exhibits broad-spectrum resistance against Fusarium virguliforme, Heterodera glycines (soybean cyst nematode), Tetranychus urticae (Koch) (spider mites), and Aphis glycines Matsumura (soybean aphids) in soybean. To understand the mechanisms of broad-spectrum immunity mediated by GmDR1, the transcriptomes of a strong and a weak GmDR1-overexpressor following treatment with chitin, a pathogen- and pest-associated molecular pattern (PAMP) common to these organisms, were investigated. The strong and weak GmDR1-overexpressors exhibited altered expression of 6098 and 992 genes, respectively, as compared to the nontransgenic control following chitin treatment. However, only 192 chitin- and 115 buffer-responsive genes exhibited over two-fold changes in expression levels in both strong and weak GmDR1-overexpressors as compared to the control. MapMan analysis of the 192 chitin-responsive genes revealed 64 biotic stress-related genes, of which 53 were induced and 11 repressed as compared to the control. The 53 chitin-induced genes include nine genes that encode receptor kinases, 13 encode nucleotide-binding leucine-rich repeat (NLR) receptor proteins, seven encode WRKY transcription factors, four ethylene response factors, and three MYB-like transcription factors. Investigation of a subset of these genes revealed three receptor protein kinases, seven NLR proteins, and one WRKY transcription factor genes that are induced following F. virguliforme and H. glycines infection. The integral plasma membrane GmDR1 protein most likely recognizes PAMPs including chitin and activates transcription of genes encoding receptor kinases, NLR proteins and defense-related genes. GmDR1 could be a pattern recognition receptor that regulates the expression of several NLRs for expression of PAMP-triggered immunity and/or priming the effector triggered immunity.
Collapse
Affiliation(s)
| | - Subodh K Srivastava
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
- USDA-ARS APDL, BARC-East Building 1040, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Wang Feifei
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, The Chinese Academy of Sciences, Harbin, 150081, China
| | | |
Collapse
|
3
|
Meshram S, Gogoi R, Bashyal BM, Mandal PK, Hossain F, Kumar A. Investigation on comparative transcriptome profiling of resistant and susceptible non-CMS maize genotypes during Bipolaris maydis race O infection. Heliyon 2024; 10:e26538. [PMID: 38434297 PMCID: PMC10907655 DOI: 10.1016/j.heliyon.2024.e26538] [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: 05/02/2023] [Revised: 01/23/2024] [Accepted: 02/15/2024] [Indexed: 03/05/2024] Open
Abstract
Maydis leaf blight is a significant disease of maize caused by Bipolaris maydis race T, O and C. Molecular mechanisms regulating defense responses in non-CMS maize towards race O fungus are not fully known. In the present investigation, comparative transcriptome profiling was conducted on a highly resistant maize genotype SC-7-2-1-2-6-1 against a standard susceptible variety CM 119 at 48 h post inoculation (h PI) along with non-infected control. mRNA sequencing generated 38.4 Gb data, where 9349602 reads were mapped uniquely in SC-7, whereas 2714725 reads were mapped uniquely in CM-119. In inoculated SC-7, the total number of differentially expressed genes (DEGs) against control was 1413, where 1011 were up-regulated, and 402 were down-regulated. In susceptible inoculated genotype CM 119, the number of DEGs against control was 2902, where 1703 were up-, and 1199 were down-regulated. DEGs between inoculated resistant and susceptible genotypes were 10745, where 5343 were up-, and 5402 were down-regulated. The RNA-seq data were validated using RT-qPCR. The key findings are that SC-7 poses a robust plant signaling system mainly induced by oxidation-reduction process and calcium-mediated signaling. It regulates its fitness-related genes efficiently, viz., aldolase 2 gene, isopropanoid, phyto hormones, P450 cytochrome, amino acid synthesis, nitrogen assimilation genes etc. These findings showed more transcriptional changes in the SC-7 genotype, which contains many defence-related genes. They can be explored in future crop development programmes to combat multiple maize diseases. The current finding provides information to elucidate molecular and cellular processes occurring in maize during B. maydis race O infection.
Collapse
Affiliation(s)
| | - Robin Gogoi
- Division of Plant Pathology, New Delhi 110 012, India
| | | | - Pranab Kumar Mandal
- ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
- ICAR- National Institute for Plant Biotechnology, New Delhi 110 012, India
| | | | - Aundy Kumar
- Division of Plant Pathology, New Delhi 110 012, India
| |
Collapse
|
4
|
Ahmed R, Dey KK, Senthil-Kumar M, Modi MK, Sarmah BK, Bhorali P. Comparative transcriptome profiling reveals differential defense responses among Alternaria brassicicola resistant Sinapis alba and susceptible Brassica rapa. FRONTIERS IN PLANT SCIENCE 2024; 14:1251349. [PMID: 38304451 PMCID: PMC10831657 DOI: 10.3389/fpls.2023.1251349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 11/14/2023] [Indexed: 02/03/2024]
Abstract
Alternaria blight is a devastating disease that causes significant crop losses in oilseed Brassicas every year. Adoption of conventional breeding to generate disease-resistant varieties has so far been unsuccessful due to the lack of suitable resistant source germplasms of cultivated Brassica spp. A thorough understanding of the molecular basis of resistance, as well as the identification of defense-related genes involved in resistance responses in closely related wild germplasms, would substantially aid in disease management. In the current study, a comparative transcriptome profiling was performed using Illumina based RNA-seq to detect differentially expressed genes (DEGs) specifically modulated in response to Alternaria brassicicola infection in resistant Sinapis alba, a close relative of Brassicas, and the highly susceptible Brassica rapa. The analysis revealed that, at 48 hpi (hours post inoculation), 3396 genes were upregulated and 23239 were downregulated, whereas at 72 hpi, 4023 genes were upregulated and 21116 were downregulated. Furthermore, a large number of defense response genes were detected to be specifically regulated as a result of Alternaria infection. The transcriptome data was validated using qPCR-based expression profiling for selected defense-related DEGs, that revealed significantly higher fold change in gene expression in S. alba when compared to B. rapa. Expression of most of the selected genes was elevated across all the time points under study with significantly higher expression towards the later time point of 72 hpi in the resistant germplasm. S. alba activates a stronger defense response reaction against the disease by deploying an array of genes and transcription factors involved in a wide range of biological processes such as pathogen recognition, signal transduction, cell wall modification, antioxidation, transcription regulation, etc. Overall, the study provides new insights on resistance of S. alba against A. brassicicola, which will aid in devising strategies for breeding resistant varieties of oilseed Brassica.
Collapse
Affiliation(s)
- Reshma Ahmed
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Kuntal Kumar Dey
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | | | - Mahendra Kumar Modi
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Bidyut Kumar Sarmah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
- Department of Biotechnology - Northeast Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Priyadarshini Bhorali
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| |
Collapse
|
5
|
Chen J, Hou S, Zhang Q, Meng J, Zhang Y, Du J, Wang C, Liang D, Guo Y. Genome-Wide Identification and Analysis of the WRKY Gene Family in Asparagus officinalis. Genes (Basel) 2023; 14:1704. [PMID: 37761844 PMCID: PMC10530708 DOI: 10.3390/genes14091704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
In recent years, the related research of the WRKY gene family has been gradually promoted, which is mainly reflected in the aspects of environmental stress and hormone response. However, to make the study of the WRKY gene family more complete, we also need to focus on the whole-genome analysis and identification of the family. In previous studies, the whole WRKY gene family of Arabidopsis, legumes and other plants has been thoroughly studied. However, since the publication of Asparagus officinalis genome-wide data, there has never been an analysis of the whole WRKY gene family. To understand more broadly the function of the WRKY gene family, the whole genome and salt stress transcriptome data of asparagus were used for comprehensive analysis in this study, including WRKY gene family identification, phylogenetic tree construction, analysis of conserved mods and gene domains, extraction of cis-acting elements, intron/exon analysis, species collinearity analysis, and WRKY expression analysis under salt stress. The results showed that a total of 70 genes were selected and randomly distributed on 10 chromosomes and one undefined chromosome. According to the functional classification of Arabidopsis thaliana, the WRKY family of asparagus was divided into 11 subgroups (C1-C9, U1, U2). It is worth considering that the distribution rules of gene-conserved motifs, gene domains and introns/exons in the same subfamily are similar, which suggests that genes in the same subfamily may regulate similar physiological processes. In this study, 11 cis-acting elements of WRKY family were selected, among which auxin, gibberellin, abscisic acid, salicylic acid and other hormone-regulated induction elements were involved. In addition, environmental stress (such as drought stress and low-temperature response) also accounted for a large proportion. Interestingly, we analyzed a total of two tandem duplicate genes and 13 segmental duplication genes, suggesting that this is related to the amplification of the WRKY gene family. Transcriptome data analysis showed that WRKY family genes could regulate plant growth and development by up-regulating and down-regulating gene expression under salt stress. Volcanic maps showed that 3 and 15 AoWRKY genes were significantly up-regulated or down-regulated in NI&NI+S and AMF&AMF+S, respectively. These results provide a new way to analyze the evolution and function of the WRKY gene family, and can provide a reference for the production and research of asparagus.
Collapse
Affiliation(s)
- Jing Chen
- College of Biological Science and Technology, Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China; (J.C.); (S.H.); (J.M.); (Y.Z.); (J.D.); (C.W.)
| | - Sijia Hou
- College of Biological Science and Technology, Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China; (J.C.); (S.H.); (J.M.); (Y.Z.); (J.D.); (C.W.)
| | - Qianqian Zhang
- Chinese Institute for Brain Research, Beijing 102206, China;
- College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jianqiao Meng
- College of Biological Science and Technology, Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China; (J.C.); (S.H.); (J.M.); (Y.Z.); (J.D.); (C.W.)
| | - Yingying Zhang
- College of Biological Science and Technology, Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China; (J.C.); (S.H.); (J.M.); (Y.Z.); (J.D.); (C.W.)
| | - Junhong Du
- College of Biological Science and Technology, Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China; (J.C.); (S.H.); (J.M.); (Y.Z.); (J.D.); (C.W.)
| | - Cong Wang
- College of Biological Science and Technology, Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China; (J.C.); (S.H.); (J.M.); (Y.Z.); (J.D.); (C.W.)
| | - Dan Liang
- College of Biological Science and Technology, Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China; (J.C.); (S.H.); (J.M.); (Y.Z.); (J.D.); (C.W.)
| | - Yunqian Guo
- College of Biological Science and Technology, Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China; (J.C.); (S.H.); (J.M.); (Y.Z.); (J.D.); (C.W.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
| |
Collapse
|
6
|
Trémulot L, Macadré C, Gal J, Garmier M, Launay-Avon A, Paysant-Le Roux C, Ratet P, Noctor G, Dufresne M. Impact of high atmospheric carbon dioxide on the biotic stress response of the model cereal species Brachypodium distachyon. FRONTIERS IN PLANT SCIENCE 2023; 14:1237054. [PMID: 37662181 PMCID: PMC10469009 DOI: 10.3389/fpls.2023.1237054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/20/2023] [Indexed: 09/05/2023]
Abstract
Losses due to disease and climate change are among the most important issues currently facing crop production. It is therefore important to establish the impact of climate change, and particularly of high carbon dioxide (hCO2), on plant immunity in cereals, which provide 60% of human calories. The aim of this study was to determine if hCO2 impacts Brachypodium distachyon immunity, a model plant for temperate cereals. Plants were grown in air (430 ppm CO2) and at two high CO2 conditions, one that is relevant to projections within the coming century (1000 ppm) and a concentration sufficient to saturate photosynthesis (3000 ppm). The following measurements were performed: phenotyping and growth, salicylic acid contents, pathogen resistance tests, and RNAseq analysis of the transcriptome. Improved shoot development was observed at both 1000 and 3000 ppm. A transcriptomic analysis pointed to an increase in primary metabolism capacity under hCO2. Alongside this effect, up-regulation of genes associated with secondary metabolism was also observed. This effect was especially evident for the terpenoid and phenylpropanoid pathways, and was accompanied by enhanced expression of immunity-related genes and accumulation of salicylic acid. Pathogen tests using the fungus Magnaporthe oryzae revealed that hCO2 had a complex effect, with enhanced susceptibility to infection but no increase in fungal development. The study reveals that immunity in B. distachyon is modulated by growth at hCO2 and allows identification of pathways that might play a role in this effect.
Collapse
Affiliation(s)
- Lug Trémulot
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
| | - Catherine Macadré
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
| | - Joséphine Gal
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
| | - Marie Garmier
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
| | - Alexandra Launay-Avon
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
| | - Christine Paysant-Le Roux
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
| | - Pascal Ratet
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
| | - Graham Noctor
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Institut Universitaire de France (IUF), Paris, France
| | - Marie Dufresne
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
| |
Collapse
|
7
|
Liu Y, Liu Q, Li X, Zhang Z, Ai S, Liu C, Ma F, Li C. MdERF114 enhances the resistance of apple roots to Fusarium solani by regulating the transcription of MdPRX63. PLANT PHYSIOLOGY 2023; 192:2015-2029. [PMID: 36721923 PMCID: PMC10315273 DOI: 10.1093/plphys/kiad057] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/04/2023] [Accepted: 01/06/2023] [Indexed: 06/18/2023]
Abstract
As the main fungal etiologic agent of apple (Malus domestica) replant disease (ARD), Fusarium solani seriously damages apple roots. Ethylene response factors (ERFs) play an important role in plant resistance to biotic stress. Here, we show that MdERF114 is expressed during F. solani infections and positively regulates the resistance of apple roots to F. solani. Yeast one-hybrid, dual-luciferase, electrophoretic mobility shift assays and determinations of lignin content indicated that MdERF114 directly binds the GCC-box of the MdPEROXIDASE63 (MdPRX63) promoter and activates its expression, resulting in lignin deposition in apple roots and increased resistance to F. solani. We identified a WRKY family transcription factor, MdWRKY75, that binds to the W-box of the MdERF114 promoter. Overexpression of MdWRKY75 enhanced resistance of apple roots to F. solani. MdMYB8 interacted with MdERF114 to enhance resistance to F. solani by promoting the binding of MdERF114 to the MdPRX63 promoter. In summary, our findings reveal that the MdWRKY75-MdERF114-MdMYB8-MdPRX63 module is required for apple resistance to F. solani and the application of this mechanism by Agrobacterium rhizogenes-mediated root transformation provides a promising strategy to prevent ARD.
Collapse
Affiliation(s)
- Yusong Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling 712100, China
| | - Qianwei Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling 712100, China
| | - Xuewen Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling 712100, China
| | - Zhijun Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling 712100, China
| | - Shukang Ai
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling 712100, China
| | - Cheng Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A & F University, Yangling 712100, China
| | | | - Chao Li
- Author for correspondence: ; (F.M.); (C.L.)
| |
Collapse
|
8
|
Zhang T, Zhang C, Zhang X, Liang Z, Xia P. Multi-algorithm cooperation research of WRKY genes under nitrogen stress in Panax notoginseng. PROTOPLASMA 2023; 260:1081-1096. [PMID: 36564534 DOI: 10.1007/s00709-022-01832-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 12/17/2022] [Indexed: 06/07/2023]
Abstract
WRKY transcription factors play an important role in the immune system and the innate defense response of plants. WRKY transcription factors have great feedback on nitrogen stress. In this study, bioinformatics was used to detect the WRKYs of Panax notoginseng (PnWRKYs). The response of PnWRKYs under nitrogen stress was also well studied. PnWRKYs were distributed on 11 chromosomes. According to PnWRKY and Arabidopsis thaliana WRKY (AtWRKY) domains, these PnWRKY proteins were divided into three groups by phylogenetic analysis. MEME analysis showed that almost every member contained motif 1 and motif 2. PlantCARE online predicted the cis-acting elements of the promoter. PnWRKY gene family members obtained 22 pairs of repeat fragments by collinearity analysis. The expression levels of PnWRKYs in different parts (roots, flowers, and leafs) were analyzed by the gene expression pattern. They reflected tissue-specific expressions. The qRT-PCR experiments were used to detect 74 PnWRKYs under nitrogen stress. The results showed that the expression levels of 8 PnWRKYs were significantly induced. The PnWRKY gene family may be involved in biotic/abiotic stresses and hormone induction. This study will not only lay the foundation to explore the functions of PnWRKYs but also provide candidate genes for the future improvement of P. notoginseng.
Collapse
Affiliation(s)
- Tingting Zhang
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Caijuan Zhang
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Xuemin Zhang
- Tianjin TASLY Modern Chinese Medicine Resources Co., Ltd, Tianjin, 300402, China
| | - Zongsuo Liang
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Pengguo Xia
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| |
Collapse
|
9
|
Zhang L, Yu Y, Zhang M, Rong K, Wu Y, Zhang M, Hu H. Genome-wide identification of xylan glucuronosyltransferase family in cotton and function characterization of GhGUX5 in regulating Verticillium wilt resistance. Int J Biol Macromol 2023:124795. [PMID: 37207759 DOI: 10.1016/j.ijbiomac.2023.124795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/26/2023] [Accepted: 04/27/2023] [Indexed: 05/21/2023]
Abstract
Xylan glucuronosyltransferase (GUX) is widely involved in a variety of physiological processes in plants, including plant development, growth and the defense response to pathogens. However, the function of GUX regulators in Verticillium dahliae (V. dahliae) infection has not been considered previously in cotton. Overall, 119 GUX genes were identified from multiple species and were phylogenetically categorized into seven classes. Duplication event analysis indicated that GUXs in Gossypium hirsutum primarily originated from segmental duplication. GhGUXs promoter analysis indicated cis-regulatory elements capable of reacting to several different stresses. RNA-Seq data and qRT-PCR analysis both indicated that most GhGUXs were associated with V. dahliae infection. Gene interaction network analysis showed that GhGUX5 interacted with 11 proteins, and the relative expression of these 11 proteins changed significantly following V. dahliae infection. In addition, silencing and overexpression of GhGUX5 results to enhance and reduce plant's susceptibility to V. dahliae. Further study showed that TRV: GhGUX5 silenced cotton plants exhibited a decrease in the degree of lignification, total lignin content, gene expression levels involved in lignin biosynthesis, and enzyme activity compared with TRV: 00. The above results indicate that GhGUX5 enhances Verticillium wilt resistance through the lignin biosynthesis pathway.
Collapse
Affiliation(s)
- Lei Zhang
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Yongang Yu
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Meng Zhang
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Kaikuo Rong
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Yanxia Wu
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Mingxia Zhang
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China.
| | - Haiyan Hu
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China.
| |
Collapse
|
10
|
Wen F, Wu X, Zhang L, Xiao J, Li T, Jia M. Molecular Cloning and Characterization of WRKY12, A Pathogen Induced WRKY Transcription Factor from Akebia trifoliata. Genes (Basel) 2023; 14:genes14051015. [PMID: 37239375 DOI: 10.3390/genes14051015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
WRKY transcription factors (TFs), which are plant-specific TFs, play significant roles in plant defense. Here, a pathogen-induced WRKY gene, named AktWRKY12, which was the homologous gene of AtWRKY12, was isolated from Akebia trifoliata. The AktWRKY12 gene has a total length of 645 nucleotides and an open reading frame (ORF) encoding 214 amino acid polypeptides. The characterizations of AktWRKY12 were subsequently performed with the ExPASy online tool Compute pI/Mw, PSIPRED and SWISS-MODEL softwares. The AktWRKY12 could be classified as a member of WRKY group II-c TFs based on sequence alignment and phylogenetic analysis. The results of tissue-specific expression analysis revealed that the AktWRKY12 gene was expressed in all the tested tissues, and the highest expression level was detected in A. trifoliata leaves. Subcellular localization analysis showed that AktWRKY12 was a nuclear protein. Results showed that the expression level of AktWRKY12 significantly increased in A. trifoliata leaves with pathogen infection. Furthermore, heterologous over-expression of AktWRKY12 in tobacco resulted in suppressed expression of lignin synthesis key enzyme genes. Based on our results, we speculate that AktWRKY12 might play a negative role in A. trifoliata responding to biotic stress by regulating the expression of lignin synthesis key enzyme genes during pathogen infection.
Collapse
Affiliation(s)
- Feng Wen
- Anhui Chuju Planting and Deep Processing Engineering Research Center, School of Biological Science and Food Engineering, Chuzhou University, Chuzhou 239000, China
| | - Xiaozhu Wu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Biopesticides and Chemical Biology, Ministry of Education, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang 332000, China
| | - Lishen Zhang
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang 332000, China
| | - Jiantao Xiao
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang 332000, China
| | - Tongjian Li
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang 332000, China
| | - Mingliang Jia
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang 332000, China
| |
Collapse
|
11
|
Kabir N, Wang X, Lu L, Qanmber G, Liu L, Si A, Zhang L, Cao W, Yang Z, Yu Y, Liu Z. Functional characterization of TBL genes revealed the role of GhTBL7 and GhTBL58 in cotton fiber elongation. Int J Biol Macromol 2023; 241:124571. [PMID: 37100328 DOI: 10.1016/j.ijbiomac.2023.124571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 04/01/2023] [Accepted: 04/14/2023] [Indexed: 04/28/2023]
Abstract
TBL (Trichome Birefringence Like) gene family members are involved in trichome initiation and xylan acetylation in several plant species. In our research, we identified 102 TBLs from G. hirsutum. The phylogenetic tree classified TBL genes into five groups. Collinearity analysis of TBL genes indicated 136 paralogous gene pairs in G. hirsutum. Gene duplication indicated that WGD or segmental duplication contributed to the GhTBL gene family expansion. Promoter cis-elements of GhTBLs were related to growth and development, seed-specific regulation, light, and stress responses. GhTBL genes (GhTBL7, GhTBL15, GhTBL21, GhTBL25, GhTBL45, GhTBL54, GhTBL67, GhTBL72, and GhTBL77) exhibited upregulated response under exposure to cold, heat, NaCl, and PEG. GhTBL genes exhibited high expression during fiber development stages. Two GhTBL genes (GhTBL7 and GhTBL58) showed differential expression at 10 DPA fiber, as 10 DPA is a fast fiber elongation stage and fiber elongation is a very important stage of cotton fiber development. Subcellular localization of GhTBL7 and GhTBL58 revealed that these genes reside inside the cell membrane. Promoter GUS activity of GhTBL7 and GhTBL58 exhibited deep staining in roots. To further validate the role of these genes in cotton fiber elongation, we silenced these genes and observed a significant reduction in the fiber length at 10 DPA. In conclusion, the functional study of cell membrane-associated genes (GhTBL7 and GhTBL58) showed deep staining in root tissues and potential function during cotton fiber elongation at 10 DPA fiber.
Collapse
Affiliation(s)
- Nosheen Kabir
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Xuwen Wang
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute, Xinjiang Academy Agricultural and Reclamation Science, Shihezi 832003, China
| | - Lili Lu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Ghulam Qanmber
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Le Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Aijun Si
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute, Xinjiang Academy Agricultural and Reclamation Science, Shihezi 832003, China
| | - Lian Zhang
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute, Xinjiang Academy Agricultural and Reclamation Science, Shihezi 832003, China
| | - Wei Cao
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute, Xinjiang Academy Agricultural and Reclamation Science, Shihezi 832003, China
| | - Zuoren Yang
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute, Xinjiang Academy Agricultural and Reclamation Science, Shihezi 832003, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Yu Yu
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute, Xinjiang Academy Agricultural and Reclamation Science, Shihezi 832003, China.
| | - Zhao Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China.
| |
Collapse
|
12
|
Zhang Y, Li P, Niu Y, Zhang Y, Wen G, Zhao C, Jiang M. Evolution of the WRKY66 Gene Family and Its Mutations Generated by the CRISPR/Cas9 System Increase the Sensitivity to Salt Stress in Arabidopsis. Int J Mol Sci 2023; 24:3071. [PMID: 36834483 PMCID: PMC9959582 DOI: 10.3390/ijms24043071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/29/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
Group Ⅲ WRKY transcription factors (TFs) play pivotal roles in responding to the diverse abiotic stress and secondary metabolism of plants. However, the evolution and function of WRKY66 remains unclear. Here, WRKY66 homologs were traced back to the origin of terrestrial plants and found to have been subjected to both motifs' gain and loss, and purifying selection. A phylogenetic analysis showed that 145 WRKY66 genes could be divided into three main clades (Clade A-C). The substitution rate tests indicated that the WRKY66 lineage was significantly different from others. A sequence analysis displayed that the WRKY66 homologs had conserved WRKY and C2HC motifs with higher proportions of crucial amino acid residues in the average abundance. The AtWRKY66 is a nuclear protein, salt- and ABA- inducible transcription activator. Simultaneously, under salt stress and ABA treatments, the superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) activities, as well as the seed germination rates of Atwrky66-knockdown plants generated by the clustered, regularly interspaced, short palindromic repeats/CRISPR-associated 9 (CRISPR/Cas9) system, were all lower than those of wild type (WT) plants, but the relative electrolyte leakage (REL) was higher, indicating the increased sensitivities of the knockdown plants to the salt stress and ABA treatments. Moreover, RNA-seq and qRT-PCR analyses revealed that several regulatory genes in the ABA-mediated signaling pathway involved in stress response of the knockdown plants were significantly regulated, being evidenced by the more moderate expressions of the genes. Therefore, the AtWRKY66 likely acts as a positive regulator in the salt stress response, which may be involved in an ABA-mediated signaling pathway.
Collapse
Affiliation(s)
- Youze Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Peng Li
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Yuqian Niu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yuxin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Guosong Wen
- Research & Development Center for Heath Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Changling Zhao
- Research & Development Center for Heath Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Min Jiang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, 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
| |
Collapse
|
13
|
Identification of the WRKY Gene Family and Characterization of Stress-Responsive Genes in Taraxacum kok-saghyz Rodin. Int J Mol Sci 2022; 23:ijms231810270. [PMID: 36142183 PMCID: PMC9499643 DOI: 10.3390/ijms231810270] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
WRKY transcription factors present unusual research value because of their critical roles in plant physiological processes and stress responses. Taraxacum kok-saghyz Rodin (TKS) is a perennial herb of dandelion in the Asteraceae family. However, the research on TKS WRKY TFs is limited. In this study, 72 TKS WRKY TFs were identified and named. Further comparison of the core motifs and the structure of the WRKY motif was analyzed. These TFs were divided into three groups through phylogenetic analysis. Genes in the same group of TkWRKY usually exhibit a similar exon-intron structure and motif composition. In addition, virtually all the TKS WRKY genes contained several cis-elements related to stress response. Expression profiling of the TkWRKY genes was assessed using transcriptome data sets and Real-Time RT-PCR data in tissues during physiological development, under abiotic stress and hormonal treatments. For instance, the TkWRKY18, TkWRKY23, and TkWRKY38 genes were significantly upregulated during cold stress, whereas the TkWRKY21 gene was upregulated under heat-stress conditions. These results could provide a basis for further studies on the function of the TKS WRKY gene family and genetic amelioration of TKS germplasm.
Collapse
|
14
|
Qiu J, Ni L, Xia X, Chen S, Zhang Y, Lang M, Li M, Liu B, Pan Y, Li J, Zhang X. Genome-Wide Analysis of the Protein Phosphatase 2C Genes in Tomato. Genes (Basel) 2022; 13:genes13040604. [PMID: 35456410 PMCID: PMC9032827 DOI: 10.3390/genes13040604] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 01/27/2023] Open
Abstract
The plant protein phosphatase 2C (PP2C) plays an irreplaceable role in phytohormone signaling, developmental processes, and manifold stresses. However, information about the PP2C gene family in tomato (Solanum lycopersicum) is relatively restricted. In this study, a genome-wide investigation of the SlPP2C gene family was performed. A total of 92 SlPP2C genes were identified, they were distributed on 11 chromosomes, and all the SlPP2C proteins have the type 2C phosphatase domains. Based on phylogenetic analysis of PP2C genes in Arabidopsis, rice, and tomato, SlPP2C genes were divided into eight groups, designated A–H, which is also supported by the analyses of gene structures and protein motifs. Gene duplication analysis revealed that the duplication of whole genome and chromosome segments was the main cause of SLPP2Cs expansion. A total of 26 cis-elements related to stress, hormones, and development were identified in the 3 kb upstream region of these SlPP2C genes. Expression profile analysis revealed that the SlPP2C genes display diverse expression patterns in various tomato tissues. Furthermore, we investigated the expression patterns of SlPP2C genes in response to Ralstonia solanacearum infection. RNA-seq and qRT-PCR data reveal that nine SlPP2Cs are correlated with R. solanacearum. The above evidence hinted that SlPP2C genes play multiple roles in tomato and may contribute to tomato resistance to bacterial wilt. This study obtained here will give an impetus to the understanding of the potential function of SlPP2Cs and lay a solid foundation for tomato breeding and transgenic resistance to plant pathogens.
Collapse
Affiliation(s)
- Jianfang Qiu
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, The Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (J.Q.); (L.N.); (X.X.); (S.C.); (Y.Z.); (M.L.); (M.L.); (B.L.); (Y.P.); (J.L.)
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Lei Ni
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, The Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (J.Q.); (L.N.); (X.X.); (S.C.); (Y.Z.); (M.L.); (M.L.); (B.L.); (Y.P.); (J.L.)
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Xue Xia
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, The Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (J.Q.); (L.N.); (X.X.); (S.C.); (Y.Z.); (M.L.); (M.L.); (B.L.); (Y.P.); (J.L.)
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Shihao Chen
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, The Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (J.Q.); (L.N.); (X.X.); (S.C.); (Y.Z.); (M.L.); (M.L.); (B.L.); (Y.P.); (J.L.)
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Yan Zhang
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, The Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (J.Q.); (L.N.); (X.X.); (S.C.); (Y.Z.); (M.L.); (M.L.); (B.L.); (Y.P.); (J.L.)
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Min Lang
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, The Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (J.Q.); (L.N.); (X.X.); (S.C.); (Y.Z.); (M.L.); (M.L.); (B.L.); (Y.P.); (J.L.)
| | - Mengyu Li
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, The Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (J.Q.); (L.N.); (X.X.); (S.C.); (Y.Z.); (M.L.); (M.L.); (B.L.); (Y.P.); (J.L.)
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Binman Liu
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, The Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (J.Q.); (L.N.); (X.X.); (S.C.); (Y.Z.); (M.L.); (M.L.); (B.L.); (Y.P.); (J.L.)
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Yu Pan
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, The Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (J.Q.); (L.N.); (X.X.); (S.C.); (Y.Z.); (M.L.); (M.L.); (B.L.); (Y.P.); (J.L.)
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Jinhua Li
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, The Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (J.Q.); (L.N.); (X.X.); (S.C.); (Y.Z.); (M.L.); (M.L.); (B.L.); (Y.P.); (J.L.)
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Xingguo Zhang
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, The Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China; (J.Q.); (L.N.); (X.X.); (S.C.); (Y.Z.); (M.L.); (M.L.); (B.L.); (Y.P.); (J.L.)
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
- Correspondence: ; Tel.: +86-23-68250974; Fax: +86-23-68251274
| |
Collapse
|
15
|
Wen F, Wu X, Li T, Jia M, Liao L. Characterization of the WRKY gene family in Akebia trifoliata and their response to Colletotrichum acutatum. BMC PLANT BIOLOGY 2022; 22:115. [PMID: 35287589 PMCID: PMC8919620 DOI: 10.1186/s12870-022-03511-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 03/04/2022] [Indexed: 05/11/2023]
Abstract
BACKGROUND Akebia trifoliata, belonging to the Lardizabalaceae family, is a well-known Chinese traditional medicinal plant, susceptible to many diseases, such as anthracnose and powdery mildew. WRKY is one of the largest plant-specific transcription factor families and plays important roles in plant growth, development and stress response, especially in disease resistance. However, little was known about the numbers, characters, evolutionary relationship and expression of WRKY genes in A. trifoliata in response to plant disease due to lacking of A. trifoliata genome. RESULTS A total of 42 putative AktWRKY genes were identified based on the full-length transcriptome-sequencing data of A. trifoliata. Then 42 AktWRKY genes were divided into three major groups (Group I-III) based on the WRKY domains. Motif analysis showed members within same group shared a similar motif composition, implying a functional conservation. Tissue-specific expression analysis showed that AktWRKY genes could be detected in all tissues, while few AktWRKY genes were tissue specific. We further evaluated the expression of AktWRKY genes in three varieties in response to Colletotrichum acutatum by qRT-PCR. The expression patterns of AktWRKY genes were similar between C01 and susceptible variety I02, but distinctly different in resistant variety H05. In addition, it showed that more than 64 percentages of AktWRKY genes were differentially expressed during fungal infection in I02 and H05. Furthermore, Gene ontology (GO) analysis showed that AktWRKY genes were categorized into 26 functional groups under cellular components, molecular functions and biological processes, and a predicted protein interaction network was also constructed. CONCLUSIONS Results of bioinformation analysis and expression patterns implied that AktWRKYs might play multiple function in response to biotic stresses. Our study could facilitate to further investigate the function and regulatory mechanism of the WRKY in A. trifoliata during pathogen response.
Collapse
Affiliation(s)
- Feng Wen
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
| | - Xiaozhu Wu
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tongjian Li
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Mingliang Jia
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Liang Liao
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| |
Collapse
|
16
|
Soliman SA, Hafez EE, Al-Kolaibe AMG, Abdel Razik ESS, Abd-Ellatif S, Ibrahim AA, Kabeil SSA, Elshafie HS. Biochemical Characterization, Antifungal Activity, and Relative Gene Expression of Two Mentha Essential Oils Controlling Fusarium oxysporum, the Causal Agent of Lycopersicon esculentum Root Rot. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11020189. [PMID: 35050077 PMCID: PMC8781374 DOI: 10.3390/plants11020189] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 05/08/2023]
Abstract
Tomato (Lycopersicon esculentum Mill.) is important food in daily human diets. Root rot disease by Fusarium oxysporum caused huge losses in tomato quality and yield annually. The extensive use of synthetic and chemical fungicides has environmental risks and health problems. Recent studies have pointed out the use of medicinal plant essential oils (EOs) and extracts for controlling fungal diseases. In the current research, Mentha spicata and Mentha longifolia EOs were used in different concentrations to control F. oxysporum. Many active compounds are present in these two EOs such as: thymol, adapic acid, menthol and menthyl acetate. These compounds possess antifungal effect through malformation and degradation of the fungal cell wall. The relative expression levels of distinctly upregulated defense-related WRKY genes (WRKY1, WRKY4, WRKY33 and WRKY53) in seedling root were evaluated as a plant-specific transcription factor (TF) group in different response pathways of abiotic stress. Results showed significant expression levels of WRKY, WRKY53, WRKY33, WRKY1 and WRKY4 genes. An upregulation was observed in defense-related genes such as chitinase and defensin in roots by application EOs under pathogen condition. In conclusion, M. spicata and M. longifolia EOs can be used effectively to control this plant pathogen as sustainable and eco-friendly botanical fungicides.
Collapse
Affiliation(s)
- Seham A. Soliman
- Plant Protection and Biomolecular Diagnosis Department, Arid Lands Cultivation Research Institute, City of Scientific Research and Technology Applications, Borg EL-Arab, Alexandria 21934, Egypt; (S.A.S.); (E.E.H.); (E.-S.S.A.R.); (A.A.I.)
| | - Elsayed E. Hafez
- Plant Protection and Biomolecular Diagnosis Department, Arid Lands Cultivation Research Institute, City of Scientific Research and Technology Applications, Borg EL-Arab, Alexandria 21934, Egypt; (S.A.S.); (E.E.H.); (E.-S.S.A.R.); (A.A.I.)
| | | | - El-Sayed S. Abdel Razik
- Plant Protection and Biomolecular Diagnosis Department, Arid Lands Cultivation Research Institute, City of Scientific Research and Technology Applications, Borg EL-Arab, Alexandria 21934, Egypt; (S.A.S.); (E.E.H.); (E.-S.S.A.R.); (A.A.I.)
| | - Sawsan Abd-Ellatif
- Bioprocess Development Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technology Applications, Borg EL-Arab, Alexandria 21934, Egypt;
| | - Amira A. Ibrahim
- Plant Protection and Biomolecular Diagnosis Department, Arid Lands Cultivation Research Institute, City of Scientific Research and Technology Applications, Borg EL-Arab, Alexandria 21934, Egypt; (S.A.S.); (E.E.H.); (E.-S.S.A.R.); (A.A.I.)
| | - Sanaa S. A. Kabeil
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technology Applications, Borg EL-Arab, Alexandria 21934, Egypt;
| | - Hazem S. Elshafie
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, Viale dell’Ateneo Lucano 10, 85100 Potenza, Italy
- Correspondence: ; Tel.: +39-0971-205522; Fax: +39-0971-205503
| |
Collapse
|
17
|
Ali F, Li Y, Li F, Wang Z. Genome-wide characterization and expression analysis of cystathionine β-synthase genes in plant development and abiotic stresses of cotton (Gossypium spp.). Int J Biol Macromol 2021; 193:823-837. [PMID: 34687765 DOI: 10.1016/j.ijbiomac.2021.10.079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 10/09/2021] [Accepted: 10/11/2021] [Indexed: 11/20/2022]
Abstract
Cystathionine β-synthase (CBS) domains containing proteins (CDCPs) form a large family and play roles in development via regulation of the thioredoxin system as well as abiotic and biotic stress responses of plant. However, the comprehensive study of CBS genes remained elusive in cotton. Here, we identified 237 CBS genes in 11 plant species and the phylogenetic analysis categorized CBS genes into four groups. Whole-genome or segmental with dispersed duplication events contributed to GhCBS gene family expansion. Moreover, orthologous/paralogous genes among three cotton species (G. hirsutum, G. arboreum, and G. raimondii) were detected from the syntenic map among eight plant species. Strong purifying selection for dicotyledonous and monocotyledonous CBS genes, and cis-elements related to plant growth and development, abiotic and hormonal response were observed. Transcriptomic data and qRT-PCR validation of 12 GhCBS genes indicated their critical role in ovule development as most of the genes showed high enrichment. Further, some of GhCBS (GhCBS5, GhCBS16, GhCBS17, GhCBS24, GhCBS25, GhCBS26, and GhCBS52) genes were regulated under various abiotic and hormonal treatments for different time points and involve in ovule and fiber development which provided key genes for future cotton breeding programs. In addition, transgenic tobacco plants overexpressing GhCBS4 transiently exhibited higher water and chlorophyll content indicating improved tolerance toward drought stress. Overall, this study provides the characterization of GhCBS genes for plant growth, abiotic and hormonal stresses, thereby, intimating their significance in cotton molecular breeding for resistant cultivars.
Collapse
Affiliation(s)
- Faiza Ali
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, 450001 Zhengzhou, China
| | - Yonghui Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, 450001 Zhengzhou, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, 450001 Zhengzhou, China; State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Zhi Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, 450001 Zhengzhou, China; State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| |
Collapse
|
18
|
Ding Y, Gardiner DM, Powell JJ, Colgrave ML, Park RF, Kazan K. Adaptive defence and sensing responses of host plant roots to fungal pathogen attack revealed by transcriptome and metabolome analyses. PLANT, CELL & ENVIRONMENT 2021; 44:3526-3544. [PMID: 34591319 DOI: 10.1111/pce.14195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 09/15/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Plant root-produced constitutive and inducible defences inhibit pathogenic microorganisms within roots and in the rhizosphere. However, regulatory mechanisms underlying host responses during root-pathogen interactions are largely unexplored. Using the model species Brachypodium distachyon (Bd), we studied transcriptional and metabolic responses altered in Bd roots following challenge with Fusarium graminearum (Fg), a fungal pathogen that causes diseases in diverse organs of cereal crops. Shared gene expression patterns were found between Bd roots and spikes during Fg infection associated with the mycotoxin deoxynivalenol (DON). Overexpression of BdMYB78, an up-regulated transcription factor, significantly increased root resistance during Fg infection. We show that Bd roots recognize encroaching Fg prior to physical contact by altering transcription of genes associated with multiple cellular processes such as reactive oxygen species and cell development. These changes coincide with altered levels of secreted host metabolites detected by an untargeted metabolomic approach. The secretion of Bd metabolites was suppressed by Fg as enhanced levels of defence-associated metabolites were found in roots during pre-contact with a Fg mutant defective in host perception and the ability to cause disease. Our results help to understand root defence strategies employed by plants, with potential implications for improving the resistance of cereal crops to soil pathogens.
Collapse
Affiliation(s)
- Yi Ding
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, St Lucia, Queensland, Australia
- The Plant Breeding Institute, School of Life & Environmental Sciences, Faculty of Science, The University of Sydney, Cobbitty, New South Wales, Australia
| | - Donald M Gardiner
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, St Lucia, Queensland, Australia
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia, Queensland, Australia
| | - Jonathan J Powell
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, St Lucia, Queensland, Australia
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia, Queensland, Australia
| | - Michelle L Colgrave
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, St Lucia, Queensland, Australia
- Australian Research Council, Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Robert F Park
- The Plant Breeding Institute, School of Life & Environmental Sciences, Faculty of Science, The University of Sydney, Cobbitty, New South Wales, Australia
| | - Kemal Kazan
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, St Lucia, Queensland, Australia
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia, Queensland, Australia
| |
Collapse
|
19
|
Li P, Li X, Jiang M. CRISPR/Cas9-mediated mutagenesis of WRKY3 and WRKY4 function decreases salt and Me-JA stress tolerance in Arabidopsis thaliana. Mol Biol Rep 2021; 48:5821-5832. [PMID: 34351541 DOI: 10.1007/s11033-021-06541-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 07/02/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND WRKY transcription factor is involved in regulation of plant growth and development, response to biotic and abiotic stresses, including homologous WRKY3 and WRKY4 genes which play a vital role in regulating plants defense response to pathogen and drought stress. METHODS AND RESULTS To investigate the function of AtWRKY3 and AtWRKY4 genes in regulating salt and Me-JA stresses, the loss-of-function mutations were generated by clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) system in Arabidopsis thaliana. Several independent transgenic lines with single or double mutations were obtained via Agrobacterium-mediated transformation. The knockout lines of AtWRKY3 and AtWRKY4 genes were successfully achieved and confirmed by qRT-PCR technology. Expression analysis showed that AtWRKY3 and AtWRKY4 genes had significantly up-regulated under salt and Me-JA stresses. The growth of double mutant plants under salt or Me-JA stresses were significantly inhibited compared with corresponding wild type (WT) plants, especially their root lengths. Moreover, the double mutant plants displayed salt and Me-JA sensitivity phenotypic characteristics, such as the increased relative electrolyte leakage (REL) and a substantial reduce in the activities of antioxidant enzymes, including superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) activities. CONCLUSION Taken together, these data suggested that the simultaneous modification of homologous gene copies of WRKY are established using CRISPR/Cas9 system in A. thaliana and the loss of AtWRKY3 and AtWRKY4 has an effect on ROS scavenging pathways to reduce stress tolerance.
Collapse
Affiliation(s)
- Peng Li
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Xiwen Li
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Min Jiang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, 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.
| |
Collapse
|
20
|
Identification, evolution and expression analysis of WRKY gene family in Eucommia ulmoides. Genomics 2021; 113:3294-3309. [PMID: 34022347 DOI: 10.1016/j.ygeno.2021.05.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 03/31/2021] [Accepted: 05/17/2021] [Indexed: 11/20/2022]
Abstract
The WRKY transcription factors is one of the largest families of transcription factors (TFs) in plants and involved in multiple biological processes. However, the role of the WRKY family had not been reported in Eucommia ulmoides. In this study, 45 WRKY genes (EuWRKY1-45) with conserved WRKY domain were identified in E. ulmoides and classified into three groups. The group II was further divided into five subgroups based on phylogenetic analysis, and each clade was well supported by the conserved motifs. All the genes were located on 34 different scaffolds respectively. A number of development-, light-, hormone-, and stress-related elements were randomly distributed in the promoter sequences of EuWRKYs. Expression profiles indicated that EuWRKY genes were involved in leaf development, and majority of EuWRKYs genes were highly expressed in leaf buds. Co-expression analysis of WRKYs suggested an intricate interplay of growth-related responses. EuWRKY4 was involved in a complex proteins interaction network. Collectively, our results provide extensive insights into the WRKY gene family, thereby contributing to the screening of additional candidate genes in E. ulmoides.
Collapse
|
21
|
Shehzad M, Zhou Z, Ditta A, Khan M, Cai X, Xu Y, Maqbool A, Khalofah A, Shaban M, Naeem M, Ansari MJ, Wang K, Liu F. Identification and characterization of genes related to salt stress tolerance within segregation distortion regions of genetic map in F2 population of upland cotton. PLoS One 2021; 16:e0247593. [PMID: 33770112 PMCID: PMC7997035 DOI: 10.1371/journal.pone.0247593] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/09/2021] [Indexed: 12/12/2022] Open
Abstract
Segregation distortion (SD) is a genetic mechanism commonly found in segregating or stable populations. The principle behind this puzzles many researchers. The F2 generation developed from wild Gossypium darwinii and G. hirsutum CCRI12 species was used to investigate the possible transcription factors within the segregation distortion regions (SDRs). The 384 out of 2763 markers were distorted in 29 SDRs on 18 chromosomes. Good collinearity was observed among genetic and physical maps of G. hirsutum and G. barbadense syntenic blocks. Total 568 genes were identified from SDRs of 18 chromosomes. Out of these genes, 128 belonged to three top-ranked salt-tolerant gene families. The DUF597 contained 8 uncharacterized genes linked to Pkinase (PF00069) gene family in the phylogenetic tree, while 15 uncharacterized genes clustered with the zinc finger gene family. Two hundred thirty four miRNAs targeted numerous genes, including ghr-miR156, ghr-miR399 and ghr-miR482, while others targeted top-ranked stress-responsive transcription factors. Moreover, these genes were involved in the regulation of numerous stress-responsive cis-regulatory elements. The RNA sequence data of fifteen upregulated genes were verified through the RT-qPCR. The expression profiles of two highly upregulated genes (Gh_D01G2015 and Gh_A01G1773) in salt-tolerant G. darwinii showed antagonistic expression in G. hirsutum. The results indicated that salt-tolerant genes have been possibly transferred from the wild G. darwinii species. A detailed functional analysis of these genes can be carried out which might be helpful in the future for gene cloning, transformation, gene editing and the development of salt-resistant cotton varieties.
Collapse
Affiliation(s)
- Muhammad Shehzad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
| | - Allah Ditta
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
- Plant Breeding, and Genetics Division, Cotton Group, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Punjab, Pakistan
| | - Majid Khan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
| | - Amir Maqbool
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Ahlam Khalofah
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Muhammad Shaban
- Department of Plant Breeding and Genetics, Faculty of Agricultural Science & Technology, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Naeem
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Mohammad Javed Ansari
- Department of Botany, Hindu College Moradabad (Mahatma Jyotiba Phule Rohilkhand University Bareilly), Bareilly, India
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
- * E-mail: (KW); (FL)
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, P.R China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- * E-mail: (KW); (FL)
| |
Collapse
|
22
|
Liu Z, Shi L, Yang S, Qiu S, Ma X, Cai J, Guan D, Wang Z, He S. A conserved double-W box in the promoter of CaWRKY40 mediates autoregulation during response to pathogen attack and heat stress in pepper. MOLECULAR PLANT PATHOLOGY 2021; 22:3-18. [PMID: 33151622 PMCID: PMC7749755 DOI: 10.1111/mpp.13004] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/01/2020] [Accepted: 09/07/2020] [Indexed: 05/11/2023]
Abstract
CaWRKY40 was previously found to be transcriptionally up-regulated by Ralstonia solanacearum inoculation (RSI) or heat stress (HS), but the underlying mechanism remains unknown. Herein, we report that a double-W box-element (DWE) in the promoter of CaWRKY40 is critical for these responses. The upstream W box unit WI of this composite element is crucial for preferential binding by CaWRKY40 and responsiveness to RSI or HS. DWE-driven CaWRKY40 can be transcriptionally and nonspecifically regulated by itself and by CaWRKY58 and CaWRKY27. The DWE was also found in the promoters of CaWRKY40 orthologs, including AtWRKY40, VvWRKY40, GmWRKY40, CplWRKY40, SaWRKY40, SpWRKY40, NtWRKY40, and NaWRKY40. DWEAtWRKY40 was analogous to DWECaWRKY40 by responding to RSI or HS and AtWRKY40 expression. These data suggest that a conserved response of plants to pathogen infection or HS is probably mediated by binding of the DWE by WRKY40.
Collapse
Affiliation(s)
- Zhi‐Qin Liu
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouChina
- College of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Lan‐Ping Shi
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouChina
- College of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Sheng Yang
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouChina
- College of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Shan‐Shan Qiu
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouChina
- College of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xiao‐Ling Ma
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouChina
- College of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jin‐Sen Cai
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouChina
- College of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - De‐Yi Guan
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouChina
- College of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Zong‐Hua Wang
- Fujian University Key Laboratory for Plant‐Microbe InteractionCollege of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhouChina
- Institute of OceanographyMinjiang UniversityFuzhouChina
| | - Shui‐Lin He
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouChina
- College of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| |
Collapse
|
23
|
Tiika RJ, Wei J, Ma R, Yang H, Cui G, Duan H, Ma Y. Identification and expression analysis of the WRKY gene family during different developmental stages in Lycium ruthenicum Murr. fruit. PeerJ 2020; 8:e10207. [PMID: 33194409 PMCID: PMC7602686 DOI: 10.7717/peerj.10207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/28/2020] [Indexed: 11/20/2022] Open
Abstract
Background The WRKY gene family, one of the major transcription factor families in plants, plays crucial regulatory roles in physiological and biological developmental processes, and the adaptation of plants to the environment. However, the systematic study of WRKY structure, expression profiling, and regulatory functions has not been extensively reported in Lycium ruthenicum, although these aspects have been comprehensively studied in most plant species. Methods In this study, the WRKY genes were identified from a L. ruthenicum transcriptome database by using bioinformatics. The identification, phylogenetic analysis, zinc-finger structures, and conserved motif prediction were extensively explored. Moreover, the expression levels of 23 selected genes with fragments per kilobase of exons per million mapped reads (FPKM) >5 were assayed during different fruit developmental stages with real-time quantitative polymerase chain reaction (RT-qPCR). Results A total of 73 putative WRKY proteins in the L. ruthenicum transcriptome database were identified and examined. Forty-four proteins with the WRKY domain were identified and divided into three major groups with several subgroups, in accordance with those in other plant species. All 44 LrWRKY proteins contained one or two conserved WRKY domains and a zinc-finger structure. Conserved motif prediction revealed conservation of the WRKY DNA-binding domain in L. ruthenicum proteins. The selected LrWRKY genes exhibited discrete expression patterns during different fruit developmental stages. Interestingly, five LrWRKYs (-20, -21, -28, -30, and -31) were expressed remarkably throughout the fruit developmental stages. Discussion Our results reveal the characteristics of the LrWRKY gene family, thus laying a foundation for further functional analysis of the WRKY family in L. ruthenicum.
Collapse
Affiliation(s)
- Richard John Tiika
- College of Forestry, Gansu Agricultural University, Lanzhou, Gansu Province, China.,Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Jia Wei
- College of Forestry, Gansu Agricultural University, Lanzhou, Gansu Province, China.,Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Rui Ma
- College of Forestry, Gansu Agricultural University, Lanzhou, Gansu Province, China
| | - Hongshan Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Guangxin Cui
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Huirong Duan
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Yanjun Ma
- College of Forestry, Gansu Agricultural University, Lanzhou, Gansu Province, China
| |
Collapse
|
24
|
Zhang L, Zhang H, Yang S. Cytosolic TaGAPC2 Enhances Tolerance to Drought Stress in Transgenic Arabidopsis Plants. Int J Mol Sci 2020; 21:ijms21207499. [PMID: 33053684 PMCID: PMC7590034 DOI: 10.3390/ijms21207499] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/02/2020] [Accepted: 10/04/2020] [Indexed: 11/16/2022] Open
Abstract
Drought is a major natural disaster that seriously affects agricultural production, especially for winter wheat in boreal China. As functional proteins, the functions and mechanisms of glyceraldehyde-3-phosphate dehydrogenase in cytoplasm (GAPCs) have remained little investigated in wheat subjected to adverse environmental conditions. In this study, we cloned and characterized a GAPC isoform TaGAPC2 in wheat. Over-expression of TaGApC2-6D in Arabidopsis led to enhanced root length, reduced reactive oxygen species (ROS) production, and elevated drought tolerance. In addition, the dual-luciferase assays showed that TaWRKY28/33/40/47 could positively regulate the expression of TaGApC2-6A and TaGApC2-6D. Further results of the yeast two-hybrid system and bimolecular fluorescence complementation assay (BiFC) demonstrate that TaPLDδ, an enzyme producing phosphatidic acid (PA), could interact with TaGAPC2-6D in plants. These results demonstrate that TaGAPC2 regulated by TaWRKY28/33/40/47 plays a crucial role in drought tolerance, which may influence the drought stress conditions via interaction with TaPLDδ. In conclusion, our results establish a new positive regulation mechanism of TaGAPC2 that helps wheat fine-tune its drought response.
Collapse
|
25
|
Ogden AJ, Wietsma TW, Winkler T, Farris Y, Myers GL, Ahkami AH. Dynamics of Global Gene Expression and Regulatory Elements in Growing Brachypodium Root System. Sci Rep 2020; 10:7071. [PMID: 32341392 PMCID: PMC7184759 DOI: 10.1038/s41598-020-63224-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 02/28/2020] [Indexed: 11/09/2022] Open
Abstract
Root systems are dynamic and adaptable organs that play critical roles in plant development. However, how roots grow and accumulate biomass during plant life cycle and in relation to shoot growth phenology remains understudied. A comprehensive time-dependent root morphological analysis integrated with molecular signatures is then required to advance our understanding of root growth and development. Here we studied Brachypodium distachyon rooting process by monitoring root morphology, biomass production, and C/N ratios during developmental stages. To provide insight into gene regulation that accompanies root growth, we generated comprehensive transcript profiles of Brachypodium whole-root system at four developmental stages. Our data analysis revealed that multiple biological processes including trehalose metabolism and various families of transcription factors (TFs) were differentially expressed in root system during plant development. In particular, the AUX/IAA, ERFs, WRKY, NAC, and MADS TF family members were upregulated as plant entered the booting/heading stage, while ARFs and GRFs were downregulated suggesting these TF families as important factors involved in specific phases of rooting, and possibly in regulation of transition to plant reproductive stages. We identified several Brachypodium candidate root biomass-promoting genes and cis-regulatory elements for further functional validations and root growth improvements in grasses.
Collapse
Affiliation(s)
- Aaron J Ogden
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA
| | - Thomas W Wietsma
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA
| | - Tanya Winkler
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA
| | - Yuliya Farris
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA
| | - Gabriel L Myers
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA
| | - Amir H Ahkami
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA.
| |
Collapse
|
26
|
Li Z, Hua X, Zhong W, Yuan Y, Wang Y, Wang Z, Ming R, Zhang J. Genome-Wide Identification and Expression Profile Analysis of WRKY Family Genes in the Autopolyploid Saccharum spontaneum. PLANT & CELL PHYSIOLOGY 2020; 61:616-630. [PMID: 31830269 DOI: 10.1093/pcp/pcz227] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 12/08/2019] [Indexed: 05/19/2023]
Abstract
WRKY is one of the largest transcription factor families in plants and plays important roles in the regulation of developmental and physiological processes. To date, the WRKY gene family has not been identified in Saccharum species because of its complex polyploid genome. In this study, a total of 294 sequences for 154 SsWRKY genes were identified in the polyploid Saccharum spontaneum genome and then named on the basis of their chromosome locations, including 13 (8.4%) genes with four alleles, 29 (18.8%) genes with three alleles and 41 (26.6%) genes with two alleles. Among them, 73.8% and 16.0% of the SsWRKY genes originated from segmental duplications and tandem duplications, respectively. The WRKY members exhibited conserved gene structures and amino acid sequences among the allelic haplotypes, which were accompanied by variations in intron sizes. Phylogenetic and collinearity analyses revealed that 27 SsWRKYs originated after the split of sorghum and Saccharum, resulting in a significantly higher number of WRKYs in sugarcane than in the proximal diploid species sorghum. The analysis of RNA-seq data revealed that SsWRKYs' expression profiles in 46 different samples including different developmental stages revealed distinct temporal and spatial patterns with 52 genes expressed in all tissues, four genes not expressed in any tissues and 21 SsWRKY genes likely to be involved in photosynthesis. The comprehensive analysis of SsWRKYs' expression will provide an important and valuable foundation for further investigation of the regulatory mechanisms of WRKYs in physiological roles in sugarcane S. spontaneum.
Collapse
Affiliation(s)
- Zhen Li
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiuting Hua
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weiming Zhong
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuan Yuan
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, Guangxi 530004, China
| | - Yongjun Wang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhengchao Wang
- Provincial Key Laboratory for Developmental Biology and Neurosciences, College of Life Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Ray Ming
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, Guangxi 530004, China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jisen Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, Guangxi 530004, China
| |
Collapse
|
27
|
Li X, Tang Y, Zhou C, Zhang L, Lv J. A Wheat WRKY Transcription Factor TaWRKY46 Enhances Tolerance to Osmotic Stress in transgenic Arabidopsis Plants. Int J Mol Sci 2020; 21:ijms21041321. [PMID: 32075313 PMCID: PMC7072902 DOI: 10.3390/ijms21041321] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 02/05/2020] [Accepted: 02/13/2020] [Indexed: 11/16/2022] Open
Abstract
WRKY transcription factors play central roles in developmental processes and stress responses of wheat. Most WRKY proteins of the same group (Group III) have a similar function in abiotic stress responses in plants. TaWRKY46, a member of Group III, was up-regulated by PEG treatment. TaWRKY46-GFP fusion proteins localize to the nucleus in wheat mesophyll protoplasts. Overexpression of TaWRKY46 enhanced osmotic stress tolerance in transgenic Arabidopsis thaliana plants, which was mainly demonstrated by transgenic Arabidopsis plants forming higher germination rate and longer root length on 1/2 Murashige and Skoog (MS) medium containing mannitol. Furthermore, the expression of several stress-related genes (P5CS1, RD29B, DREB2A, ABF3, CBF2, and CBF3) was significantly increased in TaWRKY46-overexpressing transgenic Arabidopsis plants after mannitol treatment. Taken together, these findings proposed that TaWRKY46 possesses vital functions in improving drought tolerance through ABA-dependent and ABA-independent pathways when plants are exposed to adverse osmotic conditions. TaWRKY46 can be taken as a candidate gene for transgenic breeding against osmotic stress in wheat. It can further complement and improve the information of the WRKY family members of Group III.
Collapse
Affiliation(s)
| | | | | | | | - Jinyin Lv
- Correspondence: ; Tel.: +86-135-7219-6187
| |
Collapse
|
28
|
Wen F, Ye F, Xiao Z, Liao L, Li T, Jia M, Liu X, Wu X. Genome-wide survey and expression analysis of calcium-dependent protein kinase (CDPK) in grass Brachypodium distachyon. BMC Genomics 2020; 21:53. [PMID: 31948407 PMCID: PMC6966850 DOI: 10.1186/s12864-020-6475-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 01/09/2020] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Ca2+ played as a ubiquitous secondary messenger involved in plant growth, development, and responses to various environmental stimuli. Calcium-dependent protein kinases (CDPK) were important Ca2+ sensors, which could directly translate Ca2+ signals into downstream phosphorylation signals. Considering the importance of CDPKs as Ca2+ effectors for regulation of plant stress tolerance and few studies on Brachypodium distachyon were available, it was of interest for us to isolate CDPKs from B. distachyon. RESULTS A systemic analysis of 30 CDPK family genes in B. distachyon was performed. Results showed that all BdCDPK family members contained conserved catalytic Ser/Thr protein kinase domain, autoinhibitory domain, and EF-hand domain, and a variable N-terminal domain, could be divided into four subgroup (I-IV), based upon sequence homology. Most BdCDPKs had four EF-hands, in which EF2 and EF4 revealed high variability and strong divergence from EF-hand in AtCDPKs. Synteny results indicated that large number of syntenic relationship events existed between rice and B. distachyon, implying their high conservation. Expression profiles indicated that most of BdCDPK genes were involved in phytohormones signal transduction pathways and regulated physiological process in responding to multiple environmental stresses. Moreover, the co-expression network implied that BdCDPKs might be both the activator and the repressor involved in WRKY transcription factors or MAPK cascade genes mediated stress response processes, base on their complex regulatory network. CONCLUSIONS BdCDPKs might play multiple function in WRKY or MAPK mediated abiotic stresses response and phytohormone signaling transduction in B. distachyon. Our genomics analysis of BdCDPKs could provide fundamental information for further investigation the functions of CDPKs in integrating Ca2+ signalling pathways in response to environments stresses in B. distachyon.
Collapse
Affiliation(s)
- Feng Wen
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
| | - Feng Ye
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Zhulong Xiao
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Liang Liao
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Tongjian Li
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Mingliang Jia
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Xinsheng Liu
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Xiaozhu Wu
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
| |
Collapse
|
29
|
Tolosa LN, Zhang Z. The Role of Major Transcription Factors in Solanaceous Food Crops under Different Stress Conditions: Current and Future Perspectives. PLANTS 2020; 9:plants9010056. [PMID: 31906447 PMCID: PMC7020414 DOI: 10.3390/plants9010056] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/09/2019] [Accepted: 12/21/2019] [Indexed: 01/08/2023]
Abstract
Plant growth, development, and productivity are adversely affected by environmental stresses such as drought (osmotic stress), soil salinity, cold, oxidative stress, irradiation, and diverse diseases. These impacts are of increasing concern in light of climate change. Noticeably, plants have developed their adaptive mechanism to respond to environmental stresses by transcriptional activation of stress-responsive genes. Among the known transcription factors, DoF, WRKY, MYB, NAC, bZIP, ERF, ARF and HSF are those widely associated with abiotic and biotic stress response in plants. Genome-wide identification and characterization analyses of these transcription factors have been almost completed in major solanaceous food crops, emphasizing these transcription factor families which have much potential for the improvement of yield, stress tolerance, reducing marginal land and increase the water use efficiency of solanaceous crops in arid and semi-arid areas where plant demand more water. Most importantly, transcription factors are proteins that play a key role in improving crop yield under water-deficient areas and a place where the severity of pathogen is very high to withstand the ongoing climate change. Therefore, this review highlights the role of major transcription factors in solanaceous crops, current and future perspectives in improving the crop traits towards abiotic and biotic stress tolerance and beyond. We have tried to accentuate the importance of using genome editing molecular technologies like CRISPR/Cas9, Virus-induced gene silencing and some other methods to improve the plant potential in giving yield under unfavorable environmental conditions.
Collapse
Affiliation(s)
- Lemessa Negasa Tolosa
- Key Laboratory of Agricultural Water Resources, Hebie Laboratory of Agricultural Water Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Shijiazhuang 050021, China;
- University of Chinese Academy Sciences, Beijing 100049, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences CAS, Beijing 100101, China
| | - Zhengbin Zhang
- Key Laboratory of Agricultural Water Resources, Hebie Laboratory of Agricultural Water Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Shijiazhuang 050021, China;
- University of Chinese Academy Sciences, Beijing 100049, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences CAS, Beijing 100101, China
- Correspondence:
| |
Collapse
|
30
|
Wu GQ, Li ZQ, Cao H, Wang JL. Genome-wide identification and expression analysis of the WRKY genes in sugar beet ( Beta vulgaris L.) under alkaline stress. PeerJ 2019; 7:e7817. [PMID: 31632850 PMCID: PMC6796966 DOI: 10.7717/peerj.7817] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 09/03/2019] [Indexed: 12/15/2022] Open
Abstract
Background The WRKY transcription factor family plays crucial roles in many aspects of physiological processes and adaption to environment. Although the WRKY genes have been widely identified in various plant species, the structure and function of the WRKY family in sugar beet (Beta vulgaris L.) remains unknown. Methods In the present study, the WRKY genes were identified from the sugar beet genome by bioinformatics. A phylogenetic tree was constructed by MEGA7.0. A distribution map of these genes was displayed by MapInspect 1.0. Furthermore, the exon-intron structure and the conserved motifs were predicted by GSDS 2.0 and MEME 5.0.5, respectively. Additionally, the expression levels of nine selected genes in shoots and roots of sugar beet seedlings exposed to alkaline stress were assayed by qRT-PCR. Results A total of 58 putative BvWRKY genes are identified in the sugar beet genome. The coding sequences of these genes ranged from 558 to 2,307 bp and molecular weights (MWs) varied from 21.3 to 84. The BvWRKY genes are clustered into three major groups I, II, and III, with 11, 40, and seven members, based on the primary amino acid sequences. The number of introns in the BvWRKY genes ranged from 1 to 5, with a majority of BvWRKY (27/58) containing three exons. All the BvWRKY genes have one or two conserved WRKY domains and zinc-finger structure. Moreover, the selected BvWRKY genes showed a variety of expression patterns in shoots and roots of seedlings under various concentrations of NaHCO3. Importantly, BvWRKY10 in shoots and BvWRKY16 in roots were remarkably up-regulated by alkaline stress. Taken together, our findings extend understandings of the BvWRKY genes family and provide useful information for subsequent research on their functions in sugar beet under alkaline stress.
Collapse
Affiliation(s)
- Guo-Qiang Wu
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Zhi-Qiang Li
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Han Cao
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Jin-Long Wang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, China
| |
Collapse
|
31
|
Identification and in Silico Characterization of GT Factors Involved in Phytohormone and Abiotic Stresses Responses in Brachypodium distachyon. Int J Mol Sci 2019; 20:ijms20174115. [PMID: 31450734 PMCID: PMC6747514 DOI: 10.3390/ijms20174115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/14/2019] [Accepted: 08/20/2019] [Indexed: 11/17/2022] Open
Abstract
GT factors play critical roles in plant growth and development and in response to various environmental stimuli. Considering the new functions of GT factors on the regulation of plant stress tolerance and seeing as few studies on Brachypodium distachyon were available, we identified GT genes in B. distachyon, and the gene characterizations and phylogenies were systematically analyzed. Thirty-one members of BdGT genes were distributed on all five chromosomes with different densities. All the BdGTs could be divided into five subfamilies, including GT-1, GT-2, GTγ, SH4, and SIP1, based upon their sequence homology. BdGTs exhibited considerably divergent structures among each subfamily according to gene structure and conserved functional domain analysis, but the members within the same subfamily were relatively structure-conserved. Synteny results indicated that a large number of syntenic relationship events existed between rice and B. distachyon. Expression profiles indicated that the expression levels of most of BdGT genes were changed under abiotic stresses and hormone treatments. Moreover, the co-expression network exhibited a complex regulatory network between BdGTs and BdWRKYs as well as that between BdGTs and BdMAPK cascade gene. Results showed that GT factors might play multiple functions in responding to multiple environmental stresses in B. distachyon and participate in both the positive and negative regulation of WRKY- or MAPK-mediated stress response processes. The genome-wide analysis of BdGTs and the co-regulation network under multiple stresses provide valuable information for the further investigation of the functions of BdGTs in response to environment stresses.
Collapse
|
32
|
Qanmber G, Ali F, Lu L, Mo H, Ma S, Wang Z, Yang Z. Identification of Histone H3 ( HH3) Genes in Gossypium hirsutum Revealed Diverse Expression During Ovule Development and Stress Responses. Genes (Basel) 2019; 10:genes10050355. [PMID: 31075950 PMCID: PMC6562411 DOI: 10.3390/genes10050355] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 04/28/2019] [Accepted: 04/30/2019] [Indexed: 12/23/2022] Open
Abstract
Histone acts as the core for nucleosomes and is a key protein component of chromatin. Among different histone variants, histone H3 (HH3) variants have been reported to play vital roles in plant development. However, biological information and evolutionary relationships of HH3 genes in cotton remain to be elucidated. The current study identified 34 HH3 genes in Gossypium hirsutum. Phylogenetic analysis classified HH3 genes of 19 plant species into eight distinct clades. Sequence logos analysis among Arabidopsis, rice, and G. hirsutum amino acid residues showed higher conservation in amino acids. Using collinearity analysis, we identified 81 orthologous/paralogous gene pairs among the four genomes (A, D, At, and Dt) of cotton. Further, orthologous/paralogous and the Ka/Ks ratio demonstrated that cotton HH3 genes experienced strong purifying selection pressure with restricted functional divergence resulting from segmental and whole genome duplication. Expression pattern analysis indicated that GhHH3 genes were preferentially expressed in cotton ovule tissues. Additionally, GhHH3 gene expression can be regulated by abiotic stresses (cold, heat, sodium chloride (NaCl), and polyethylene glycol (PEG)) and phytohormonal (brassinolide (BL), gibberellic acid (GA), indole-3-acetic acid (IAA), salicylic acid (SA), and methyl jasmonate (MeJA)) treatments, suggesting that GhHH3 genes might play roles in abiotic and hormone stress resistance. Taken together, this work provides important information to decipher complete molecular and physiological functions of HH3 genes in cotton.
Collapse
Affiliation(s)
- Ghulam Qanmber
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Faiza Ali
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Lili Lu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Huijuan Mo
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Shuya Ma
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Zhi Wang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
- Zhengzhou Reseach Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 4550001, China.
| | - Zuoren Yang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
- Zhengzhou Reseach Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 4550001, China.
| |
Collapse
|
33
|
Nan H, Gao LZ. Genome-Wide Analysis of WRKY Genes and Their Response to Hormone and Mechanic Stresses in Carrot. Front Genet 2019; 10:363. [PMID: 31191596 PMCID: PMC6504813 DOI: 10.3389/fgene.2019.00363] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 04/05/2019] [Indexed: 11/13/2022] Open
Abstract
The WRKY gene family plays a vital role in plant development and environment response. Although previous studies suggested that the WRKY genes in carrot (Kuroda type) involved in biotic and abiotic stress responses, the information of WRKY genes in the latest version of the carrot genome (Daucus carota v2.0, Nantes type carrot) and their response to hormone and injury stresses have not been reported. In this study, we performed a genome-wide analysis of WRKYs using a chromosome-scale genome assembly of carrot (Daucus carota subsp. sativus L.). We identified a total of 67 WRKY genes, which were further classified into the three groups. These WRKY genes are unevenly distributed on carrot chromosomes. We found that more than half of them were derived from whole-genome duplication (WGD) events, suggesting that WGDs have played a major role during the evolution of the WRKY gene family. We experimentally ascertained the expression divergence existed between WGD-derived WRKY duplicated gene pairs, which is indicative of functional differentiation between duplicated genes. Our analysis of cis-acting elements indicated that WRKY genes were transcriptionally regulated upon hormone and mechanic injury stresses. Gene expression analyses by qRT-PCR further presented that WRKY genes were involved in hormone and mechanic injury stresses.
Collapse
Affiliation(s)
- Hong Nan
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Li-Zhi Gao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.,Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| |
Collapse
|
34
|
Genome-Wide Identification and Characterization of the PERK Gene Family in Gossypium hirsutum Reveals Gene Duplication and Functional Divergence. Int J Mol Sci 2019; 20:ijms20071750. [PMID: 30970629 PMCID: PMC6479967 DOI: 10.3390/ijms20071750] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/27/2019] [Accepted: 04/01/2019] [Indexed: 12/20/2022] Open
Abstract
Proline-rich extensin-like receptor kinases (PERKs) are an important class of receptor kinases in plants. Receptor kinases comprise large gene families in many plant species, including the 15 PERK genes in Arabidopsis. At present, there is no comprehensive published study of PERK genes in G. hirsutum. Our study identified 33 PERK genes in G. hirsutum. Phylogenetic analysis of conserved PERK protein sequences from 15 plant species grouped them into four well defined clades. The GhPERK gene family is an evolutionarily advanced gene family that lost its introns over time. Several cis-elements were identified in the promoter regions of the GhPERK genes that are important in regulating growth, development, light responses and the response to several stresses. In addition, we found evidence for gene loss or addition through segmental or whole genome duplication in cotton. Gene duplication and synteny analysis identified 149 orthologous/paralogous gene pairs. Ka/Ks values show that most GhPERK genes experienced strong purifying selection during the rapid evolution of the gene family. GhPERK genes showed high expression levels in leaves and during ovule development. Furthermore, the expression of GhPERK genes can be regulated by abiotic stresses and phytohormone treatments. Additionally, PERK genes could be involved in several molecular, biological and physiological processes that might be the result of functional divergence.
Collapse
|
35
|
Identification and Expression Profiling of Protein Phosphatases ( PP2C) Gene Family in Gossypium hirsutum L. Int J Mol Sci 2019; 20:ijms20061395. [PMID: 30897702 PMCID: PMC6471114 DOI: 10.3390/ijms20061395] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/16/2019] [Accepted: 03/18/2019] [Indexed: 01/02/2023] Open
Abstract
The protein phosphatase (PP2C) gene family, known to participate in cellular processes, is one of the momentous and conserved plant-specific gene families that regulate signal transduction in eukaryotic organisms. Recently, PP2Cs were identified in Arabidopsis and various other crop species, but analysis of PP2C in cotton is yet to be reported. In the current research, we found 87 (Gossypiumarboreum), 147 (Gossypiumbarbadense), 181 (Gossypiumhirsutum), and 99 (Gossypiumraimondii) PP2C-encoding genes in total from the cotton genome. Herein, we provide a comprehensive analysis of the PP2C gene family in cotton, such as gene structure organization, gene duplications, expression profiling, chromosomal mapping, protein motif organization, and phylogenetic relationships of each species. Phylogenetic analysis further categorized PP2C genes into 12 subgroups based on conserved domain composition analysis. Moreover, we observed a strong signature of purifying selection among duplicated pairs (i.e., segmental and dispersed) of Gossypiumhirsutum. We also observed the tissue-specific response of GhPP2C genes in organ and fiber development by comparing the RNA-sequence (RNA-seq) data reported on different organs. The qRT-PCR validation of 30 GhPP2C genes suggested their critical role in cotton by exposure to heat, cold, drought, and salt stress treatments. Hence, our findings provide an overview of the PP2C gene family in cotton based on various bioinformatic tools that demonstrated their critical role in organ and fiber development, and abiotic stress tolerance, thereby contributing to the genetic improvement of cotton for the resistant cultivar.
Collapse
|
36
|
Haider MS, Khan N, Pervaiz T, Zhongjie L, Nasim M, Jogaiah S, Mushtaq N, Jiu S, Jinggui F. Genome-wide identification, evolution, and molecular characterization of the PP2C gene family in woodland strawberry. Gene 2019; 702:27-35. [PMID: 30890476 DOI: 10.1016/j.gene.2019.03.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/09/2019] [Accepted: 03/14/2019] [Indexed: 12/11/2022]
Abstract
The protein phosphatase 2C (PP2C) gene family is one of the momentous and conserved plant-specific gene families, known to participate in cellular processes via reversible protein phosphorylation and regulates signal transduction in eukaryotic organisms. Recently, PP2Cs were identified in Arabidopsis and maize, however, the whole-genome analysis of PP2C in strawberry has not yet been reported. In the current research, we found 62 PP2C-encoding genes in total from the strawberry genome. Further, the phylogenetic analysis categorized FvPP2C genes into twelve subgroups with significant structural conservation based on conserved domain and amino acid sequence. Moreover, we observed a strong signature of purifying selection between the comparison of orthologous gene pairs of strawberry and Arabidopsis. The comparison of RNA-sequence (RNA-seq) data published on various vegetative and reproductive tissues of strawberry plant suggested the significant role of FvPP2C genes in organ development. The qRT-PCR validation of thirty FvPP2C genes indicated their critical tolerance-related role under abiotic stress stimuli in strawberry. Finally, the subcellular localization of FvPP2C51 gene proves that it resides and stimulates its function in the nucleus. Our findings provide an overview of the identification of strawberry FvPP2C gene family and demonstrate their critical role in tissue-specific response and abiotic stress-tolerance, thereby, intimating their significance in the strawberry molecular breeding for the resistant cultivars.
Collapse
Affiliation(s)
- Muhammad Salman Haider
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Nadeem Khan
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Tariq Pervaiz
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Liu Zhongjie
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Maazullah Nasim
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Sudisha Jogaiah
- Laboratory of Plant Healthcare and Diagnostics, P.G. Department of Biotechnology and Microbiology, Karnataka University, Dharwad, India
| | - Naveed Mushtaq
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Songtao Jiu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Fang Jinggui
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China.
| |
Collapse
|
37
|
Tan S, Gao L, Li T, Chen L. Phylogenetic and expression analysis of histone acetyltransferases in Brachypodium distachyon. Genomics 2019; 111:1966-1976. [PMID: 30641128 DOI: 10.1016/j.ygeno.2019.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 12/12/2018] [Accepted: 01/08/2019] [Indexed: 10/27/2022]
Abstract
Histone acetylation is an important post-translational modification in eukaryotes and is regulated by two antagonistic enzymes, namely histone acetyltransferase (HAT) and histone deacetylase (HDAC). However, little has been done on the HAT superfamily in Brachypodium distachyon (B. distachyon), a new model plant of Poaceae. In this study, eight HATs were identified from B. distachyon and classified into four major families. Subcellular localization analysis showed that a majority of BdHATs were predominantly localized in the nucleus. Syntenic and phylogenetic analysis indicated there may be two common ancestral CREB-binding protein (p300/CBP, HAC) genes prior to the separation of monocots and dicots. Expression analysis revealed that the potential roles of BdHATs in B. distachyon development and responses to four abiotic stresses. Protein-protein network analysis identified some potential interactive genes with BdHATs. Thus, our results will provide solid basis for further study the function of HAT genes in B. distachyon and other monocot plants.
Collapse
Affiliation(s)
- Shenglong Tan
- School of Information and Communication Engineering, Hubei University of Economics, Wuhan 430205, China
| | - Lifen Gao
- The Institute for Systems Biology, Jianghan University, Wuhan 430056, China
| | - Tiantian Li
- The Institute for Systems Biology, Jianghan University, Wuhan 430056, China.
| | - Lihong Chen
- The Institute for Systems Biology, Jianghan University, Wuhan 430056, China.
| |
Collapse
|
38
|
Srivastava R, Kumar S, Kobayashi Y, Kusunoki K, Tripathi P, Kobayashi Y, Koyama H, Sahoo L. Comparative genome-wide analysis of WRKY transcription factors in two Asian legume crops: Adzuki bean and Mung bean. Sci Rep 2018; 8:16971. [PMID: 30451872 PMCID: PMC6243003 DOI: 10.1038/s41598-018-34920-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 10/26/2018] [Indexed: 02/07/2023] Open
Abstract
The seminal participation of WRKY transcription factors in plant development, metabolism and in the governance of defense mechanism implicated their gaining importance for genomic and functional studies. The recent release of draft genome sequences of two legume crops, Adzuki bean (Vigna angularis) and Mung bean (Vigna radiata) has paved the way for characterization of WRKY gene family in these crops. We found 84 WRKY genes in Adzuki bean (VaWRKY) and 85 WRKY genes in Mung bean (VrWRKY). Based on the phylogenetic analysis, VaWRKY genes were classified into three groups with 15 members in Group I, 56 members in Group II, and 13 members in Group III, which was comparable to VrWRKY distribution in Mung bean, 16, 56 and 13 members in Group I, II and III, respectively. The few tandem and segmental duplication events suggested that recent duplication plays no prominent role in the expansion VaWRKY and VrWRKY genes. The illustration of gene-structure and their encoded protein-domains further revealed the nature of WRKY proteins. Moreover, the identification of abiotic or biotic stress-responsive cis-regulatory elements in the promoter regions of some WRKY genes provides fundamental insights for their further implementation in stress-tolerance and genetic improvement of agronomic traits.
Collapse
Affiliation(s)
- Richa Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, India
| | - Sanjeev Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, India
| | - Yasufumi Kobayashi
- Japan International Research Center for Agricultural Sciences Biological Resources, Post-Harvest Division, 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
| | - Kazutaka Kusunoki
- Faculty of Applied Biological Sciences, Gifu University, 1-1, Yanagido, 501-1193, Gifu, Japan
| | - Prateek Tripathi
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Yuriko Kobayashi
- Faculty of Applied Biological Sciences, Gifu University, 1-1, Yanagido, 501-1193, Gifu, Japan
| | - Hiroyuki Koyama
- Faculty of Applied Biological Sciences, Gifu University, 1-1, Yanagido, 501-1193, Gifu, Japan
| | - Lingaraj Sahoo
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, India.
| |
Collapse
|
39
|
Fan C, Yao H, Qiu Z, Ma H, Zeng B. Genome-wide analysis of Eucalyptus grandis WRKY genes family and their expression profiling in response to hormone and abiotic stress treatment. Gene 2018; 678:38-48. [PMID: 30077764 DOI: 10.1016/j.gene.2018.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 07/26/2018] [Accepted: 08/01/2018] [Indexed: 11/30/2022]
Abstract
The WRKY transcription factors, a large family of proteins in plants, are involved in multiple developmental and biological processes including response to phytohormones and abiotic stress. However, little information is available regarding the WRKY family in Eucalyptus, which has been the most widely planted hardwood trees in tropical and subtropical areas. In this study, a total of 79 WRKY genes (named as EgrWRKY1-79) were identified from the Eucalyptus grandis genome and classified into three main groups according to the phylogenetic analysis, which was further supported by their gene structure and conserved motifs. Of which, 28 EgrWRKYs were involved in tandem duplication but none for segmental duplication, indicating that tandem duplication was the main cause for the expansion of WRKY gene family in E. grandis. Subsequently, expression profiles of EgrWRKY genes in eight different tissues and in response to treatments of three hormones (SA, JA, and BR) and two abiotic stresses (salt and cold) were analyzed. The results revealed that the EgrWRKY genes had differential expression in their transcript abundance and they were differentially expressed in response to plant hormones and salt and cold stresses, suggesting their contributions to plant developmental processes as well as abiotic stresses with the involvement of hormone signaling transduction. Taken together, these findings will increase our understanding of EgrWRKY gene family involved in abiotic stresses and hormone signaling transduction, and also will provide some stress-responsive candidate EgrWRKY genes for further characterization of their functions in Eucalyptus.
Collapse
Affiliation(s)
- Chunjie Fan
- Key Laboratory of State Forestry Administration on Tropical Forest Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, People's Republic of China; State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, People's Republic of China
| | - Hairong Yao
- Key Laboratory of State Forestry Administration on Tropical Forest Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, People's Republic of China; College of Environment and Plant Protection, Hainan University, Haikou 570208, People's Republic of China
| | - Zhenfei Qiu
- Key Laboratory of State Forestry Administration on Tropical Forest Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, People's Republic of China; State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, People's Republic of China
| | - Haibin Ma
- Key Laboratory of State Forestry Administration on Tropical Forest Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, People's Republic of China
| | - Bingshan Zeng
- Key Laboratory of State Forestry Administration on Tropical Forest Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, People's Republic of China.
| |
Collapse
|
40
|
Xie T, Chen C, Li C, Liu J, Liu C, He Y. Genome-wide investigation of WRKY gene family in pineapple: evolution and expression profiles during development and stress. BMC Genomics 2018; 19:490. [PMID: 29940851 PMCID: PMC6019807 DOI: 10.1186/s12864-018-4880-x] [Citation(s) in RCA: 179] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 06/18/2018] [Indexed: 11/17/2022] Open
Abstract
Background WRKY proteins comprise a large family of transcription factors that play important roles in many aspects of physiological processes and adaption to environment. However, little information was available about the WRKY genes in pineapple (Ananas comosus), an important tropical fruits. The recent release of the whole-genome sequence of pineapple allowed us to perform a genome-wide investigation into the organization and expression profiling of pineapple WRKY genes. Results In the present study, 54 pineapple WRKY (AcWRKY) genes were identified and renamed on the basis of their respective chromosome distribution. According to their structural and phylogenetic features, the 54 AcWRKYs were further classified into three main groups with several subgroups. The segmental duplication events played a major role in the expansion of pineapple WRKY gene family. Synteny analysis and phylogenetic comparison of group III WRKY genes provided deep insight into the evolutionary characteristics of pineapple WRKY genes. Expression profiles derived from transcriptome data and real-time quantitative PCR analysis exhibited distinct expression patterns of AcWRKY genes in various tissues and in response to different abiotic stress and hormonal treatments. Conclusions Fifty four WRKY genes were identified in pineapple and the structure of their encoded proteins, their evolutionary characteristics and expression patterns were examined in this study. This systematic analysis provided a foundation for further functional characterization of WRKY genes with an aim of pineapple crop improvement. Electronic supplementary material The online version of this article (10.1186/s12864-018-4880-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Tao Xie
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, 510642, China.,College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Chengjie Chen
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, 510642, China.,College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Chuhao Li
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, 510642, China.,College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Jiarou Liu
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, 510642, China.,College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Chaoyang Liu
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, 510642, China. .,College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.
| | - Yehua He
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, 510642, China. .,College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.
| |
Collapse
|
41
|
Zhou X, Wu X, Li T, Jia M, Liu X, Zou Y, Liu Z, Wen F. Identification, characterization, and expression analysis of auxin response factor (ARF) gene family in Brachypodium distachyon. Funct Integr Genomics 2018; 18:709-724. [PMID: 29926224 DOI: 10.1007/s10142-018-0622-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 06/03/2018] [Accepted: 06/07/2018] [Indexed: 11/30/2022]
Abstract
Auxin response factors (ARFs) are one type of essential family of transcription factors that bind with auxin response elements (AuxRE), and play vital roles in variety of plant development and physiological processes. Brachypodium distachyon, related to the major cereal grain species, were recently developed to be a good model organism for functional genomics research. So far, genome-wide overview of the ARF gene family in B. distachyon was not available. Here, a systemic analysis of ARF gene family members in B. distachyon was performed. A comprehensive overview of the characterization of the BdARFs was obtained by multiple bioinformatics analyses, including the gene and protein structure, chromosome locations, conserved motifs of proteins, phylogenetic analysis, and cis-elements in promoters of BdARF. Results showed that all BdARFs contained conserved DBD, MR, and CTD could be divided into four classes, Ia, IIa, IIb, and III. Expression profiles of BdARF genes indicated that they were expressed across various tissues and organs, which could be clustered into three main expression groups, and most of BdARF genes were involved in phytohormone signal transduction pathways and regulated physiological process in responding to multiple environmental stresses. And predicted regulatory network between B. distachyon ARFs and IAAs was also discussed. Our genomics analysis of BdARFs could yield new insights into the complexity of the control of BdARF genes and lead to potential applications in the investigation of the accurate regulatory mechanisms of ARFs in herbaceous plants.
Collapse
Affiliation(s)
- Xiaojian Zhou
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Xiaozhu Wu
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Tongjian Li
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Mingliang Jia
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Xinshen Liu
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Yulan Zou
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Zixia Liu
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Feng Wen
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
| |
Collapse
|
42
|
Wan Y, Mao M, Wan D, Yang Q, Yang F, Li G, Wang R. Identification of the WRKY gene family and functional analysis of two genes in Caragana intermedia. BMC PLANT BIOLOGY 2018; 18:31. [PMID: 29426284 PMCID: PMC5807834 DOI: 10.1186/s12870-018-1235-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 01/14/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND WRKY transcription factors, one of the largest families of transcriptional regulators in plants, play important roles in plant development and various stress responses. The WRKYs of Caragana intermedia are still not well characterized, although many WRKYs have been identified in various plant species. RESULTS We identified 53 CiWRKY genes from C. intermedia transcriptome data, 28 of which exhibited complete open reading frames (ORFs). These CiWRKYs were divided into three groups via phylogenetic analysis according to their WRKY domains and zinc finger motifs. Conserved domain analysis showed that the CiWRKY proteins contain a highly conserved WRKYGQK motif and two variant motifs (WRKYGKK and WKKYEEK). The subcellular localization of CiWRKY26 and CiWRKY28-1 indicated that these two proteins localized exclusively to nuclei, supporting their role as transcription factors. The expression patterns of the 28 CiWRKYs with complete ORFs were examined through quantitative real-time PCR (qRT-PCR) in various tissues and under different abiotic stresses (drought, cold, salt, high-pH and abscisic acid (ABA)). The results showed that each CiWRKY responded to at least one stress treatment. Furthermore, overexpression of CiWRKY75-1 and CiWRKY40-4 in Arabidopsis thaliana suppressed the drought stress tolerance of the plants and delayed leaf senescence, respectively. CONCLUSIONS Fifty-three CiWRKY genes from the C. intermedia transcriptome were identified and divided into three groups via phylogenetic analysis. The expression patterns of the 28 CiWRKYs under different abiotic stresses suggested that each CiWRKY responded to at least one stress treatment. Overexpression of CiWRKY75-1 and CiWRKY40-4 suppressed the drought stress tolerance of Arabidopsis and delayed leaf senescence, respectively. These results provide a basis for the molecular mechanism through which CiWRKYs mediate stress tolerance.
Collapse
Affiliation(s)
- Yongqing Wan
- College of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Mingzhu Mao
- College of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Dongli Wan
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Key Laboratory of Grassland Ecology and Restoration, Ministry of Agriculture, Hohhot, China
| | - Qi Yang
- College of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Feiyun Yang
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Guojing Li
- College of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Ruigang Wang
- College of Life Sciences, Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| |
Collapse
|
43
|
Chen S, Niu X, Guan Y, Li H. Genome-Wide Analysis and Expression Profiles of the MYB Genes in Brachypodium distachyon. PLANT & CELL PHYSIOLOGY 2017; 58:1777-1788. [PMID: 29016897 DOI: 10.1093/pcp/pcx115] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 08/04/2017] [Indexed: 05/21/2023]
Abstract
MYB transcription factors are widespread in plants and play key roles in plant development. Although MYB transcription factors have been thoroughly characterized in many plants, genome-wide analysis of the MYB gene family has not yet been undertaken in Brachypodium distachyon. In this study, 122 BdMYB transcription factors were identified, comprising 85 MYB-R2R3, 34 MYB-related and three MYB-R1R2R3. Phylogenetic analysis showed that BdMYBs, OsMYBs and AtMYBs with similar functions were clustered in the same subgroup, and the phylogenetic relationships of BdMYB transcription factors were supported by highly conserved motifs and gene structures. Two cis-elements were found in the promoters of BdMYB genes. One is related to plant growth/development, the other is related to stress responses. Gene Ontology (GO) analysis indicated that most of the BdMYB genes are involved in various biological processes. The chromosome distribution pattern strongly indicated that genome-wide tandem and segment duplication mainly contributed to the expansion of the BdMYB gene family. Synteny analysis showed that 56, 58 and 61 BdMYB genes were orthologous to rice, maize and sorghum, respectively. We further demonstrated that BdMYB genes have evolved under strong purifying selection. The expression profiles indicated that most BdMYB genes might participate in floral development and respond to abiotic stresses. Additionally, 338 pairs of proteins were predicted to interact by constructing the interaction network. This work laid the foundation and provided clues for understanding the biological functions of these transcription factors.
Collapse
Affiliation(s)
- Shoukun Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Xin Niu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Yuxiang Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Haifeng Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| |
Collapse
|
44
|
Wu M, Liu H, Han G, Cai R, Pan F, Xiang Y. A moso bamboo WRKY gene PeWRKY83 confers salinity tolerance in transgenic Arabidopsis plants. Sci Rep 2017; 7:11721. [PMID: 28916739 PMCID: PMC5601430 DOI: 10.1038/s41598-017-10795-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 08/15/2017] [Indexed: 11/24/2022] Open
Abstract
The WRKY family are transcription factors, involved in plant development, and response to biotic and abiotic stresses. Moso bamboo is an important bamboo that has high ecological, economic and cultural value and is widely distributed in the south of China. In this study, we performed a genome-wide identification of WRKY members in moso bamboo and identified 89 members. By comparative analysis in six grass genomes, we found the WRKY gene family may have experienced or be experiencing purifying selection. Based on relative expression levels among WRKY IIc members under three abiotic stresses, PeWRKY83 functioned as a transcription factor and was selected for detailed analysis. The transgenic Arabidopsis of PeWRKY83 showed superior physiological properties compared with the WT under salt stress. Overexpression plants were less sensitive to ABA at both germination and postgermination stages and accumulated more endogenous ABA under salt stress conditions. Further studies demonstrated that overexpression of PeWRKY83 could regulate the expression of some ABA biosynthesis genes (AtAAO3, AtNCED2, AtNCED3), signaling genes (AtABI1, AtPP2CA) and responsive genes (AtRD29A, AtRD29B, AtABF1) under salt stress. Together, these results suggested that PeWRKY83 functions as a novel WRKY-related TF which plays a positive role in salt tolerance by regulating stress-induced ABA synthesis.
Collapse
Affiliation(s)
- Min Wu
- National Engineering Laboratory of Crop Stresses Resistance Breeding, Anhui Agricultural University, Hefei, 230036, China
| | - Huanlong Liu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Guomin Han
- National Engineering Laboratory of Crop Stresses Resistance Breeding, Anhui Agricultural University, Hefei, 230036, China
| | - Ronghao Cai
- National Engineering Laboratory of Crop Stresses Resistance Breeding, Anhui Agricultural University, Hefei, 230036, China
| | - Feng Pan
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Yan Xiang
- National Engineering Laboratory of Crop Stresses Resistance Breeding, Anhui Agricultural University, Hefei, 230036, China. xiangyanahau.@sina.com.,Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. xiangyanahau.@sina.com
| |
Collapse
|
45
|
Li L, Mu S, Cheng Z, Cheng Y, Zhang Y, Miao Y, Hou C, Li X, Gao J. Characterization and expression analysis of the WRKY gene family in moso bamboo. Sci Rep 2017; 7:6675. [PMID: 28751687 PMCID: PMC5532226 DOI: 10.1038/s41598-017-06701-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 06/16/2017] [Indexed: 12/11/2022] Open
Abstract
The WRKY family of transcription factors (TFs) is one of the ten largest families of TFs in higher plants and has been implicated in multiple biological processes. Here, we identified 121 WRKY TFs in moso bamboo, including five novel members that were not annotated in the Phyllostachys edulis genomic database. Estimation of the divergence time of paralogous gene pairs revealed an important role of the recent whole-genome duplication in the expansion of the WRKY family. Expression analysis based on quantitative reverse-transcription polymerase chain reaction (qRT-PCR) data revealed that a large number of PheWRKY genes varied significantly under cold or drought stress treatments, which could be defined as abiotic stress-responsive genes. The overexpression of PheWRKY72-2 in Arabidopsis resulted in a decreased sensitivity to drought stress during early seedling growth. PheWRKY72-2 may enhance plant tolerance to stress by functioning as a positive regulator of stoma closure. Our study provides a theoretical foundation and some experimental evidence for further functional verification of the PheWRKY family of TFs.
Collapse
Affiliation(s)
- Long Li
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, 100102, People's Republic of China.,College of Forestry, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Shaohua Mu
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, 100102, People's Republic of China
| | - Zhanchao Cheng
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, 100102, People's Republic of China
| | - Yuanwen Cheng
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, 100102, People's Republic of China
| | - Ying Zhang
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, 100102, People's Republic of China
| | - Ying Miao
- Center for Molecular Cell and Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Chenglin Hou
- Department of Microbiology, College of Life Science, Capital Normal University, Beijing, 100048, People's Republic of China
| | - Xueping Li
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, 100102, People's Republic of China.
| | - Jian Gao
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, Beijing, 100102, People's Republic of China.
| |
Collapse
|
46
|
Zhang C, Wang D, Yang C, Kong N, Shi Z, Zhao P, Nan Y, Nie T, Wang R, Ma H, Chen Q. Genome-wide identification of the potato WRKY transcription factor family. PLoS One 2017; 12:e0181573. [PMID: 28727761 PMCID: PMC5519183 DOI: 10.1371/journal.pone.0181573] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 07/03/2017] [Indexed: 12/05/2022] Open
Abstract
WRKY transcription factors play pivotal roles in regulation of stress responses. This study identified 79 WRKY genes in potato (Solanum tuberosum). Based on multiple sequence alignment and phylogenetic relationships, WRKY genes were classified into three major groups. The majority of WRKY genes belonged to Group II (52 StWRKYs), Group III had 14 and Group I consisted of 13. The phylogenetic tree further classified Group II into five sub-groups. All StWRKY genes except StWRKY79 were mapped on potato chromosomes, with eight tandem duplication gene pairs and seven segmental duplication gene pairs found from StWRKY family genes. The expression analysis of 22 StWRKYs showed their differential expression levels under various stress conditions. Cis-element prediction showed that a large number of elements related to drought, heat and salicylic acid were present in the promotor regions of StWRKY genes. The expression analysis indicated that seven StWRKYs seemed to respond to stress (heat, drought and salinity) and salicylic acid treatment. These genes are candidates for abiotic stress signaling for further research.
Collapse
Affiliation(s)
- Chao Zhang
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
| | - Dongdong Wang
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
| | - Chenghui Yang
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
| | - Nana Kong
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
| | - Zheng Shi
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
| | - Peng Zhao
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
| | - Yunyou Nan
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
| | - Tengkun Nie
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
| | - Ruoqiu Wang
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
| | - Haoli Ma
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
- * E-mail: (HM); (QC)
| | - Qin Chen
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
- * E-mail: (HM); (QC)
| |
Collapse
|
47
|
Wen F, Wu X, Li T, Jia M, Liu X, Li P, Zhou X, Ji X, Yue X. Genome-wide survey of heat shock factors and heat shock protein 70s and their regulatory network under abiotic stresses in Brachypodium distachyon. PLoS One 2017; 12:e0180352. [PMID: 28683139 PMCID: PMC5500289 DOI: 10.1371/journal.pone.0180352] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 06/14/2017] [Indexed: 11/18/2022] Open
Abstract
The heat shock protein 70s (Hsp70s) and heat shock factors (Hsfs) play key roles in protecting plant cells or tissues from various abiotic stresses. Brachypodium distachyon, recently developed an excellent model organism for functional genomics research, is related to the major cereal grain species. Although B. distachyon genome has been fully sequenced, the information of Hsf and Hsp70 genes and especially the regulatory network between Hsfs and Hsp70s remains incomplete. Here, a total of 24 BdHsfs and 29 BdHsp70s were identified in the genome by bioinformatics analysis and the regulatory network between Hsfs and Hsp70s were performed in this study. Based on highly conserved domain and motif analysis, BdHsfs were grouped into three classes, and BdHsp70s divided into six groups, respectively. Most of Hsf proteins contain five conserved domains: DBD, HR-A/B region, NLS and NES motifs and AHA domain, while Hsp70 proteins have three conserved domains: N-terminal nucleotide binding domain, peptide binding domain and a variable C-terminal lid region. Expression data revealed a large number of BdHsfs and BdHsp70s were induced by HS challenge, and a previous heat acclimation could induce the acquired thermotolerance to help seedling suffer the severe HS challenge, suggesting that the BdHsfs and BdHsp70s played a role in alleviating the damage by HS. The comparison revealed that, most BdHsfs and BdHsp70s genes responded to multiple abiotic stresses in an overlapping relationship, while some of them were stress specific response genes. Moreover, co-expression relationships and predicted protein-protein interaction network implied that class A and B Hsfs played as activator and repressors, respectively, suggesting that BdHsp70s might be regulated by both the activation and the repression mechanisms under stress condition. Our genomics analysis of BdHsfs and BdHsp70s provides important evolutionary and functional characterization for further investigation of the accurate regulatory mechanisms among Hsfs and Hsp70s in herbaceous plants.
Collapse
Affiliation(s)
- Feng Wen
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
- * E-mail:
| | - Xiaozhu Wu
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Tongjian Li
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Mingliang Jia
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Xinshen Liu
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Peng Li
- Shanghai Chenshan Plant Science Research Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS). Shanghai Chenshan Botanic Garden, Songjiang, Shanghai, China
| | - Xiaojian Zhou
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Xinxin Ji
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Xiaomin Yue
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| |
Collapse
|
48
|
Jiang J, Ma S, Ye N, Jiang M, Cao J, Zhang J. WRKY transcription factors in plant responses to stresses. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:86-101. [PMID: 27995748 DOI: 10.1111/jipb.12513] [Citation(s) in RCA: 487] [Impact Index Per Article: 69.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/16/2016] [Indexed: 05/20/2023]
Abstract
The WRKY gene family is among the largest families of transcription factors (TFs) in higher plants. By regulating the plant hormone signal transduction pathway, these TFs play critical roles in some plant processes in response to biotic and abiotic stress. Various bodies of research have demonstrated the important biological functions of WRKY TFs in plant response to different kinds of biotic and abiotic stresses and working mechanisms. However, very little summarization has been done to review their research progress. Not just important TFs function in plant response to biotic and abiotic stresses, WRKY also participates in carbohydrate synthesis, senescence, development, and secondary metabolites synthesis. WRKY proteins can bind to W-box (TGACC (A/T)) in the promoter of its target genes and activate or repress the expression of downstream genes to regulate their stress response. Moreover, WRKY proteins can interact with other TFs to regulate plant defensive responses. In the present review, we focus on the structural characteristics of WRKY TFs and the research progress on their functions in plant responses to a variety of stresses.
Collapse
Affiliation(s)
- Jingjing Jiang
- State Key Laboratory of Agrobiotechnology Shenzhen Base, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China
| | - Shenghui Ma
- State Key Laboratory of Agrobiotechnology Shenzhen Base, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
| | - Nenghui Ye
- State Key Laboratory of Agrobiotechnology Shenzhen Base, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China
| | - Ming Jiang
- Ecology Key Discipline of Zhejiang Province, College of Life Science, Taizhou University, Jiaojiang 318000, China
| | - Jiashu Cao
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
| | - Jianhua Zhang
- State Key Laboratory of Agrobiotechnology Shenzhen Base, Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| |
Collapse
|
49
|
Aamir M, Singh VK, Meena M, Upadhyay RS, Gupta VK, Singh S. Structural and Functional Insights into WRKY3 and WRKY4 Transcription Factors to Unravel the WRKY-DNA (W-Box) Complex Interaction in Tomato ( Solanum lycopersicum L.). A Computational Approach. FRONTIERS IN PLANT SCIENCE 2017; 8:819. [PMID: 28611792 PMCID: PMC5447077 DOI: 10.3389/fpls.2017.00819] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 05/01/2017] [Indexed: 05/20/2023]
Abstract
The WRKY transcription factors (TFs), play crucial role in plant defense response against various abiotic and biotic stresses. The role of WRKY3 and WRKY4 genes in plant defense response against necrotrophic pathogens is well-reported. However, their functional annotation in tomato is largely unknown. In the present work, we have characterized the structural and functional attributes of the two identified tomato WRKY transcription factors, WRKY3 (SlWRKY3), and WRKY4 (SlWRKY4) using computational approaches. Arabidopsis WRKY3 (AtWRKY3: NP_178433) and WRKY4 (AtWRKY4: NP_172849) protein sequences were retrieved from TAIR database and protein BLAST was done for finding their sequential homologs in tomato. Sequence alignment, phylogenetic classification, and motif composition analysis revealed the remarkable sequential variation between, these two WRKYs. The tomato WRKY3 and WRKY4 clusters with Solanum pennellii showing the monophyletic origin and evolution from their wild homolog. The functional domain region responsible for sequence specific DNA-binding occupied in both proteins were modeled [using AtWRKY4 (PDB ID:1WJ2) and AtWRKY1 (PDBID:2AYD) as template protein structures] through homology modeling using Discovery Studio 3.0. The generated models were further evaluated for their accuracy and reliability based on qualitative and quantitative parameters. The modeled proteins were found to satisfy all the crucial energy parameters and showed acceptable Ramachandran statistics when compared to the experimentally resolved NMR solution structures and/or X-Ray diffracted crystal structures (templates). The superimposition of the functional WRKY domains from SlWRKY3 and SlWRKY4 revealed remarkable structural similarity. The sequence specific DNA binding for two WRKYs was explored through DNA-protein interaction using Hex Docking server. The interaction studies found that SlWRKY4 binds with the W-box DNA through WRKYGQK with Tyr408, Arg409, and Lys419 with the initial flanking sequences also get involved in binding. In contrast, the SlWRKY3 made interaction with RKYGQK along with the residues from zinc finger motifs. Protein-protein interactions studies were done using STRING version 10.0 to explore all the possible protein partners involved in associative functional interaction networks. The Gene ontology enrichment analysis revealed the functional dimension and characterized the identified WRKYs based on their functional annotation.
Collapse
Affiliation(s)
- Mohd Aamir
- Department of Botany, Centre for Advanced Study, Institute of Science, Banaras Hindu UniversityVaranasi, India
| | - Vinay K. Singh
- Centre for Bioinformatics, School of Biotechnology, Institute of Science, Banaras Hindu UniversityVaranasi, India
| | - Mukesh Meena
- Department of Botany, Centre for Advanced Study, Institute of Science, Banaras Hindu UniversityVaranasi, India
| | - Ram S. Upadhyay
- Department of Botany, Centre for Advanced Study, Institute of Science, Banaras Hindu UniversityVaranasi, India
| | - Vijai K. Gupta
- Department of Chemistry and Biotechnology, ERA Chair of Green Chemistry, Tallinn University of TechnologyTallinn, Estonia
| | - Surendra Singh
- Department of Botany, Centre for Advanced Study, Institute of Science, Banaras Hindu UniversityVaranasi, India
- *Correspondence: Surendra Singh
| |
Collapse
|
50
|
Mohanta TK, Park YH, Bae H. Novel Genomic and Evolutionary Insight of WRKY Transcription Factors in Plant Lineage. Sci Rep 2016; 6:37309. [PMID: 27853303 PMCID: PMC5112548 DOI: 10.1038/srep37309] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/27/2016] [Indexed: 11/22/2022] Open
Abstract
The evolutionarily conserved WRKY transcription factor (TF) regulates different aspects of gene expression in plants, and modulates growth, development, as well as biotic and abiotic stress responses. Therefore, understanding the details regarding WRKY TFs is very important. In this study, large-scale genomic analyses of the WRKY TF gene family from 43 plant species were conducted. The results of our study revealed that WRKY TFs could be grouped and specifically classified as those belonging to the monocot or dicot plant lineage. In this study, we identified several novel WRKY TFs. To our knowledge, this is the first report on a revised grouping system of the WRKY TF gene family in plants. The different forms of novel chimeric forms of WRKY TFs in the plant genome might play a crucial role in their evolution. Tissue-specific gene expression analyses in Glycine max and Phaseolus vulgaris showed that WRKY11-1, WRKY11-2 and WRKY11-3 were ubiquitously expressed in all tissue types, and WRKY15-2 was highly expressed in the stem, root, nodule and pod tissues in G. max and P. vulgaris.
Collapse
Affiliation(s)
- Tapan Kumar Mohanta
- Free Major of Natural Sciences, College of Basic Studies, Yeungnam University, Gyeongsan, 38541, Republic of Korea
| | - Yong-Hwan Park
- School of Biotechnology, Yeungnam University, Gyeongsan, 38541, Republic of Korea
| | - Hanhong Bae
- School of Biotechnology, Yeungnam University, Gyeongsan, 38541, Republic of Korea
| |
Collapse
|