101
|
Kong W, Ding L, Cheng J, Wang B. Identification and expression analysis of genes with pathogen-inducible cis-regulatory elements in the promoter regions in Oryza sativa. RICE (NEW YORK, N.Y.) 2018; 11:52. [PMID: 30209707 PMCID: PMC6135729 DOI: 10.1186/s12284-018-0243-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 09/05/2018] [Indexed: 05/11/2023]
Abstract
BACKGROUND Complex co-regulatory networks in plants may elicit responses during pathogen infections. A number of genes are activated when these responses take place. Identification of these genes would shed new light on understanding the mechanisms of rice response to pathogen infections and the elucidation of crosstalk among diverse signaling networks in rice disease resistance/susceptibility. RESULTS Here we report the identification of genes with pathogen-inducible cis-regulatory elements (PICEs) (AS-1, G-box, GCC-box, and H-box) in the promoter regions in rice. Our results showed that a set of 882 rice genes contained these four elements in their promoter regions. Of these genes, 190 encode disease resistance/susceptibility related proteins, and 70 encode transcription factors. Analyses of the available microarray data demonstrated that 357 transcripts were differentially expressed after pathogen infections. 48 out of 53 differentially expressed transcription factors are up-regulated or down-regulated by more than 1.1-fold in response to pathogen infections. Analyses of the public mRNA-Seq data showed that 327 transcripts were differently expressed after pathogen infections. A total of 100 up-regulated genes and 37 down-regulated genes were found in common between the microarray and mRNA-Seq data. CONCLUSIONS We report here a set of rice genes that contain the four PICEs, i.e., AS-1, G-box, GCC-box, and H-box, in their promoter regions, of which, 53.5% were up- or down-regulated when pathogens attack. The PICEs in the gene promoters are critical for rice response to pathogen infections. They are also useful markers for identification of rice genes involved in response to pathogen infections.
Collapse
Affiliation(s)
- Weiwen Kong
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 Jiangsu China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Li Ding
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Jia Cheng
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Bin Wang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 Jiangsu China
| |
Collapse
|
102
|
Zhou XT, Jia LJ, Wang HY, Zhao P, Wang WY, Liu N, Song SW, Wu Y, Su L, Zhang J, Zhong NQ, Xia GX. The potato transcription factor StbZIP61 regulates dynamic biosynthesis of salicylic acid in defense against Phytophthora infestans infection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:1055-1068. [PMID: 29952082 DOI: 10.1111/tpj.14010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/10/2018] [Accepted: 06/12/2018] [Indexed: 05/21/2023]
Abstract
Salicylic acid (SA) signalling plays an essential role in plant innate immunity. In this study, we identified a component in the SA signaling pathway in potato (Solanum tuberosum), the transcription factor StbZIP61, and characterized its function in defence against Phytophthora infestans. Expression of StbZIP61 was induced upon P. infestans infection and following exposure to the defense signaling hormones SA, ethylene and jasmonic acid. Overexpression of StbZIP61 increased the tolerance of potato plants to P. infestans while RNA interference (RNAi) increased susceptibility. Yeast two-hybrid and pull down experiments revealed that StbZIP61 could interact with an NPR3-like protein (StNPR3L) that inhibited its DNA-binding and transcriptional activation activities. Moreover, StNPR3L interacted with StbZIP61 in an SA-dependent manner. Among candidate genes involved in SA-regulated defense responses, StbZIP61 had a significant impact on expression of StICS1, which encodes a key enzyme for SA biosynthesis. StICS1 transcription was induced upon P. infestans infection and this responsive expression to the pathogen was reduced in StbZIP61 RNAi plants. Accordingly, StICS1 expression was remarkably enhanced in StbZIP61-overexpressing plants. Together, our data demonstrate that StbZIP61 functions in concert with StNPR3L to regulate the temporal activation of SA biosynthesis, which contributes to SA-mediated immunity against P. infestans infection in potato.
Collapse
Affiliation(s)
- Xin-Tong Zhou
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Plant Genomics, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Jia Jia
- Institute of biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- National Laboratory of Biomacromolecules, Beijing, 100101, China
| | - Hai-Yun Wang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Plant Genomics, Beijing, 100101, China
| | - Pan Zhao
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Plant Genomics, Beijing, 100101, China
| | - Wen-Yan Wang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Plant Genomics, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ning Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Plant Genomics, Beijing, 100101, China
| | - Shuang-Wei Song
- State Key Laboratory of Plant Genomics, Beijing, 100101, China
- Yunnan Agriculture University, Kunming, 650201, China
| | - Yao Wu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Plant Genomics, Beijing, 100101, China
| | - Lei Su
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Plant Genomics, Beijing, 100101, China
| | - Jie Zhang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Plant Genomics, Beijing, 100101, China
| | - Nai-Qin Zhong
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Plant Genomics, Beijing, 100101, China
| | - Gui-Xian Xia
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Plant Genomics, Beijing, 100101, China
| |
Collapse
|
103
|
Sakr S, Wang M, Dédaldéchamp F, Perez-Garcia MD, Ogé L, Hamama L, Atanassova R. The Sugar-Signaling Hub: Overview of Regulators and Interaction with the Hormonal and Metabolic Network. Int J Mol Sci 2018; 57:2367-2379. [PMID: 30149541 DOI: 10.1093/pcp/pcw157] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/07/2018] [Accepted: 09/05/2016] [Indexed: 05/25/2023] Open
Abstract
Plant growth and development has to be continuously adjusted to the available resources. Their optimization requires the integration of signals conveying the plant metabolic status, its hormonal balance, and its developmental stage. Many investigations have recently been conducted to provide insights into sugar signaling and its interplay with hormones and nitrogen in the fine-tuning of plant growth, development, and survival. The present review emphasizes the diversity of sugar signaling integrators, the main molecular and biochemical mechanisms related to the sugar-signaling dependent regulations, and to the regulatory hubs acting in the interplay of the sugar-hormone and sugar-nitrogen networks. It also contributes to compiling evidence likely to fill a few knowledge gaps, and raises new questions for the future.
Collapse
Affiliation(s)
- Soulaiman Sakr
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | - Ming Wang
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | - Fabienne Dédaldéchamp
- Equipe "Sucres & Echanges Végétaux-Environnement", Ecologie et Biologie des Interactions, Université de Poitiers, UMR CNRS 7267 EBI, Bâtiment B31, 3 rue Jacques Fort, TSA 51106, 86073 Poitiers CEDEX 9, France.
| | - Maria-Dolores Perez-Garcia
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | - Laurent Ogé
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | - Latifa Hamama
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | - Rossitza Atanassova
- Equipe "Sucres & Echanges Végétaux-Environnement", Ecologie et Biologie des Interactions, Université de Poitiers, UMR CNRS 7267 EBI, Bâtiment B31, 3 rue Jacques Fort, TSA 51106, 86073 Poitiers CEDEX 9, France.
| |
Collapse
|
104
|
Sakr S, Wang M, Dédaldéchamp F, Perez-Garcia MD, Ogé L, Hamama L, Atanassova R. The Sugar-Signaling Hub: Overview of Regulators and Interaction with the Hormonal and Metabolic Network. Int J Mol Sci 2018; 19:ijms19092506. [PMID: 30149541 PMCID: PMC6165531 DOI: 10.3390/ijms19092506] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/07/2018] [Accepted: 08/13/2018] [Indexed: 12/31/2022] Open
Abstract
Plant growth and development has to be continuously adjusted to the available resources. Their optimization requires the integration of signals conveying the plant metabolic status, its hormonal balance, and its developmental stage. Many investigations have recently been conducted to provide insights into sugar signaling and its interplay with hormones and nitrogen in the fine-tuning of plant growth, development, and survival. The present review emphasizes the diversity of sugar signaling integrators, the main molecular and biochemical mechanisms related to the sugar-signaling dependent regulations, and to the regulatory hubs acting in the interplay of the sugar-hormone and sugar-nitrogen networks. It also contributes to compiling evidence likely to fill a few knowledge gaps, and raises new questions for the future.
Collapse
Affiliation(s)
- Soulaiman Sakr
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | - Ming Wang
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | - Fabienne Dédaldéchamp
- Equipe "Sucres & Echanges Végétaux-Environnement", Ecologie et Biologie des Interactions, Université de Poitiers, UMR CNRS 7267 EBI, Bâtiment B31, 3 rue Jacques Fort, TSA 51106, 86073 Poitiers CEDEX 9, France.
| | - Maria-Dolores Perez-Garcia
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | - Laurent Ogé
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | - Latifa Hamama
- Institut de Recherche en Horticulture et Semences, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QUASAV, F-49045 Angers, France.
| | - Rossitza Atanassova
- Equipe "Sucres & Echanges Végétaux-Environnement", Ecologie et Biologie des Interactions, Université de Poitiers, UMR CNRS 7267 EBI, Bâtiment B31, 3 rue Jacques Fort, TSA 51106, 86073 Poitiers CEDEX 9, France.
| |
Collapse
|
105
|
Ashrafi-Dehkordi E, Alemzadeh A, Tanaka N, Razi H. Meta-analysis of transcriptomic responses to biotic and abiotic stress in tomato. PeerJ 2018; 6:e4631. [PMID: 30038850 PMCID: PMC6054068 DOI: 10.7717/peerj.4631] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 03/27/2018] [Indexed: 12/23/2022] Open
Abstract
A wide range of biotic stresses (BS) and abiotic stresses (AS) adversely affect plant growth and productivity worldwide. The study of individual genes cannot be considered as an effective approach for the understanding of tolerance mechanisms, since these stresses are frequent and often in combination with each other, and a large number of genes are involved in these mechanisms. The availability of high-throughput genomic data has enabled the discovery of the role of transcription factors (TFs) in regulatory networks. A meta-analysis of BS and AS responses was performed by analyzing a total of 391 microarray samples from 23 different experiments and 2,336 differentially expressed genes (DEGs) involved in multiple stresses were identified. We identified 1,862 genes differentially regulated in response to BS was much greater than that regulated by AS, 835 genes, and found 15.4% or 361 DEGs with the conserved expression between AS and BS. The greatest percent of genes related to the cellular process (>76% genes), metabolic process (>76% genes) and response to stimulus (>50%). About 4.2% of genes involved in BS and AS responses belonged to the TF families. We identified several genes, which encode TFs that play an important role in AS and BS responses. These proteins included Jasmonate Ethylene Response Factor 1 (JERF1), SlGRAS6, MYB48, SlERF4, EIL2, protein LATE ELONGATED HYPOCOTYL (LHY), SlERF1, WRKY 26, basic leucine zipper TF, inducer of CBF expression 1-like, pti6, EIL3 and WRKY 11. Six of these proteins, JERF1, MYB48, protein LHY, EIL3, EIL2 and SlGRAS6, play central roles in these mechanisms. This research promoted a new approach to clarify the expression profiles of various genes under different conditions in plants, detected common genes from differentially regulated in response to these conditions and introduced them as candidate genes for improving plant tolerance through genetic engineering approach.
Collapse
Affiliation(s)
- Elham Ashrafi-Dehkordi
- Department of Crop Production and Plant Breeding, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Abbas Alemzadeh
- Department of Crop Production and Plant Breeding, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Nobukazu Tanaka
- Center of Gene Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan
| | - Hooman Razi
- Department of Crop Production and Plant Breeding, School of Agriculture, Shiraz University, Shiraz, Iran
| |
Collapse
|
106
|
Wang Y, Zhang Y, Zhou R, Dossa K, Yu J, Li D, Liu A, Mmadi MA, Zhang X, You J. Identification and characterization of the bZIP transcription factor family and its expression in response to abiotic stresses in sesame. PLoS One 2018; 13:e0200850. [PMID: 30011333 PMCID: PMC6047817 DOI: 10.1371/journal.pone.0200850] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/03/2018] [Indexed: 11/18/2022] Open
Abstract
Basic leucine zipper (bZIP) gene family is one of the largest transcription factor families in plants, and members of this family play important roles in multiple biological processes such as light signaling, seed maturation, flower development as well as abiotic and biotic stress responses. Nonetheless, genome-wide comprehensive analysis of the bZIP family is lacking in the important oil crop sesame. In the present study, 63 bZIP genes distributed on 14 linkage groups were identified in sesame, and denominated as SibZIP01-SibZIP63. Besides, all members of SibZIP family were divided into nine groups based on the phylogenetic relationship of Arabidopsis bZIPs, which was further supported by the analysis of their conserved motifs and gene structures. Promoter analysis showed that all SibZIP genes harbor cis-elements related to stress responsiveness in their promoter regions. Expression analyses of SibZIP genes based on transcriptome data showed that these genes have different expression patterns in different tissues. Additionally, we showed that a majority of SibZIPs (85.71%) exhibited significant transcriptional changes in responses to abiotic stresses, including drought, waterlogging, osmotic, salt, and cold, suggesting that SibZIPs may play a cardinal role in the regulation of stress responses in sesame. Together, these results provide new insights into stress-responsive SibZIP genes and pave the way for future studies of SibZIPs-mediated abiotic stress response in sesame.
Collapse
Affiliation(s)
- Yanyan Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yujuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
- Cotton Research Center, Cotton Research Center, Shandong Academy of Agricultural Sciences, Huanghuaihai Key Laboratory of Cotton Genetic Improvement and Cultivation Physiology of the Ministry of Agriculture, Jinan, China
| | - Rong Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Komivi Dossa
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
- Centre d’Etude Régional pour l’Amélioration de l’Adaptation à la Sécheresse (CERAAS), Thiès, Sénégal
| | - Jingyin Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Donghua Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Aili Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Marie Ali Mmadi
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
- Centre d’Etude Régional pour l’Amélioration de l’Adaptation à la Sécheresse (CERAAS), Thiès, Sénégal
| | - Xiurong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
- * E-mail:
| |
Collapse
|
107
|
Zhang B, Liu J, Yang ZE, Chen EY, Zhang CJ, Zhang XY, Li FG. Genome-wide analysis of GRAS transcription factor gene family in Gossypium hirsutum L. BMC Genomics 2018; 19:348. [PMID: 29743013 PMCID: PMC5944045 DOI: 10.1186/s12864-018-4722-x] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 04/24/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cotton is a major fiber and oil crop worldwide. Cotton production, however, is often threatened by abiotic environmental stresses. GRAS family proteins are among the most abundant transcription factors in plants and play important roles in regulating root and shoot development, which can improve plant resistance to abiotic stresses. However, few studies on the GRAS family have been conducted in cotton. Recently, the G. hirsutum genome sequences have been released, which provide us an opportunity to analyze the GRAS family in G. hirsutum. RESULTS In total, 150 GRAS proteins from G. hirsutum were identified. Phylogenetic analysis showed that these GRAS protins could be classified into 14 subfamilies including SCR, DLT, OS19, LAS, SCL4/7, OS4, OS43, DELLA, PAT1, SHR, HAM, SCL3, LISCL and G_GRAS. The gene structure and motif distribution analysis of the GRAS members in G. hirsutum revealed that many genes of the SHR subfamily have more than one intron, which maybe a kind of form in the evolution of plant by obtaining or losing introns. Chromosomal location and duplication analysis revealed that segment and tandem duplication maybe the reasons of the expension of the GRAS family in cotton. Gene expression analysis confirmed the expression level of GRAS members were up-regulated under different abiotic stresses, suggesting that their possible roles in response to stresses. What's more, higher expression level in root, stem, leaf and pistil also indicated these genes may have effect on the development and breeding of cotton. CONCLUSIONS This study firstly shows the comprehensive analysis of GRAS members in G. hirsutum. Our results provide important information about GRAS family and a framework for stress-resistant breeding in G. hirsutum.
Collapse
Affiliation(s)
- Bin Zhang
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, China.,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - J Liu
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhao E Yang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Er Y Chen
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Chao J Zhang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xue Y Zhang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Fu G Li
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, 455000, China. .,Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| |
Collapse
|
108
|
Hsieh JF, Chuah A, Patel HR, Sandhu KS, Foley WJ, Külheim C. Transcriptome Profiling of Melaleuca quinquenervia Challenged by Myrtle Rust Reveals Differences in Defense Responses Among Resistant Individuals. PHYTOPATHOLOGY 2018; 108:495-509. [PMID: 29135360 DOI: 10.1094/phyto-09-17-0307-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Plants have developed complex defense mechanisms to protect themselves against pathogens. A wide-host-range fungus, Austropuccinia psidii, which has caused severe damage to ecosystems and plantations worldwide, is a major threat to Australian ecosystems dominated by members of the family Myrtaceae. In particular, the east coast wetland foundation tree species Melaleuca quinquenervia, appears to be variably susceptible to this pathogen. Understanding the molecular basis of host resistance would enable better management of this rust disease. We identified resistant and susceptible individuals of M. quinquenervia and explored their differential gene expression in order to discover the molecular basis of resistance against A. psidii. Rust screening of germplasm showed a varying degree of response, with fully resistant to highly susceptible individuals. We used transcriptome profiling in samples collected before and at 5 days postinoculation (dpi). Differential gene expression analysis showed that numerous defense-related genes were induced in susceptible plants at 5 dpi. Mapping reads against the A. psidii genome showed that only susceptible plants contained fungal-derived transcripts. Resistant plants exhibited an overexpression of candidate A. psidii resistance-related genes such as receptor-like kinases, nucleotide-binding site leucine-rich repeat proteins, glutathione S-transferases, WRKY transcriptional regulators, and pathogenesis-related proteins. We identified large differences in the expression of defense-related genes among resistant individuals.
Collapse
Affiliation(s)
- Ji-Fan Hsieh
- First, fifth, and sixth authors: Research School of Biology, The Australian National University, 116 Daley Road, Canberra 2601, ACT, Australia; second and third authors: The John Curtin School of Medical Research, The Australian National University, 131 Garran Road, Canberra 2601, ACT, Australia; and fourth author: Plant Breeding Institute, The University of Sydney, 107 Cobbitty Road, Cobbitty 2570, NSW, Australia
| | - Aaron Chuah
- First, fifth, and sixth authors: Research School of Biology, The Australian National University, 116 Daley Road, Canberra 2601, ACT, Australia; second and third authors: The John Curtin School of Medical Research, The Australian National University, 131 Garran Road, Canberra 2601, ACT, Australia; and fourth author: Plant Breeding Institute, The University of Sydney, 107 Cobbitty Road, Cobbitty 2570, NSW, Australia
| | - Hardip R Patel
- First, fifth, and sixth authors: Research School of Biology, The Australian National University, 116 Daley Road, Canberra 2601, ACT, Australia; second and third authors: The John Curtin School of Medical Research, The Australian National University, 131 Garran Road, Canberra 2601, ACT, Australia; and fourth author: Plant Breeding Institute, The University of Sydney, 107 Cobbitty Road, Cobbitty 2570, NSW, Australia
| | - Karanjeet S Sandhu
- First, fifth, and sixth authors: Research School of Biology, The Australian National University, 116 Daley Road, Canberra 2601, ACT, Australia; second and third authors: The John Curtin School of Medical Research, The Australian National University, 131 Garran Road, Canberra 2601, ACT, Australia; and fourth author: Plant Breeding Institute, The University of Sydney, 107 Cobbitty Road, Cobbitty 2570, NSW, Australia
| | - William J Foley
- First, fifth, and sixth authors: Research School of Biology, The Australian National University, 116 Daley Road, Canberra 2601, ACT, Australia; second and third authors: The John Curtin School of Medical Research, The Australian National University, 131 Garran Road, Canberra 2601, ACT, Australia; and fourth author: Plant Breeding Institute, The University of Sydney, 107 Cobbitty Road, Cobbitty 2570, NSW, Australia
| | - Carsten Külheim
- First, fifth, and sixth authors: Research School of Biology, The Australian National University, 116 Daley Road, Canberra 2601, ACT, Australia; second and third authors: The John Curtin School of Medical Research, The Australian National University, 131 Garran Road, Canberra 2601, ACT, Australia; and fourth author: Plant Breeding Institute, The University of Sydney, 107 Cobbitty Road, Cobbitty 2570, NSW, Australia
| |
Collapse
|
109
|
Li N, Wei S, Chen J, Yang F, Kong L, Chen C, Ding X, Chu Z. OsASR2 regulates the expression of a defence-related gene, Os2H16, by targeting the GT-1 cis-element. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:771-783. [PMID: 28869785 PMCID: PMC5814579 DOI: 10.1111/pbi.12827] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 08/23/2017] [Indexed: 05/11/2023]
Abstract
The GT-1 cis-element widely exists in many plant gene promoters. However, the molecular mechanism that underlies the response of the GT-1 cis-element to abiotic and biotic stresses remains elusive in rice. We previously isolated a rice short-chain peptide-encoding gene, Os2H16, and demonstrated that it plays important roles in both disease resistance and drought tolerance. Here, we conducted a promoter assay of Os2H16 and identified GT-1 as an important cis-element that mediates Os2H16 expression in response to pathogen attack and osmotic stress. Using the repeated GT-1 as bait, we characterized an abscisic acid, stress and ripening 2 (ASR2) protein from yeast-one hybridization screening. Sequence alignments showed that the carboxy-terminal domain of OsASR2 containing residues 80-138 was the DNA-binding domain. Furthermore, we identified that OsASR2 was specifically bound to GT-1 and activated the expression of the target gene Os2H16, as well as GFP driven by the chimeric promoter of 2 × GT-1-35S mini construct. Additionally, the expression of OsASR2 was elevated by pathogens and osmotic stress challenges. Overexpression of OsASR2 enhanced the resistance against Xanthomonas oryzae pv. oryzae and Rhizoctonia solani, and tolerance to drought in rice. These results suggest that the interaction between OsASR2 and GT-1 plays an important role in the crosstalk of the response of rice to biotic and abiotic stresses.
Collapse
Affiliation(s)
- Ning Li
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTaianShandongChina
| | - Shutong Wei
- Shandong Provincial Key Laboratory for Biology of Vegetable Disease and Insect PestsCollege of Plant ProtectionShandong Agricultural UniversityTaianShandongChina
| | - Jing Chen
- Shandong Provincial Key Laboratory for Biology of Vegetable Disease and Insect PestsCollege of Plant ProtectionShandong Agricultural UniversityTaianShandongChina
| | - Fangfang Yang
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTaianShandongChina
| | - Lingguang Kong
- Shandong Provincial Key Laboratory for Biology of Vegetable Disease and Insect PestsCollege of Plant ProtectionShandong Agricultural UniversityTaianShandongChina
| | - Cuixia Chen
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTaianShandongChina
| | - Xinhua Ding
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTaianShandongChina
- Shandong Provincial Key Laboratory for Biology of Vegetable Disease and Insect PestsCollege of Plant ProtectionShandong Agricultural UniversityTaianShandongChina
| | - Zhaohui Chu
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTaianShandongChina
| |
Collapse
|
110
|
Zhou Y, Tang Q, Wu M, Mou D, Liu H, Wang S, Zhang C, Ding L, Luo J. Comparative transcriptomics provides novel insights into the mechanisms of selenium tolerance in the hyperaccumulator plant Cardamine hupingshanensis. Sci Rep 2018; 8:2789. [PMID: 29434336 PMCID: PMC5809607 DOI: 10.1038/s41598-018-21268-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 01/31/2018] [Indexed: 12/18/2022] Open
Abstract
Selenium (Se) is an essential mineral element for animals and humans. Cardamine hupingshanensis (Brassicaceae), found in the Wuling mountain area of China, has been identified as a novel Se hyperaccumulator plant. However, the mechanism for selenium tolerance in Cardamine plants remains unknown. In this study, two cDNA libraries were constructed from seedlings of C. hupingshanensis treated with selenite. Approximately 100 million clean sequencing reads were de novo assembled into 48,989 unigenes, of which 39,579 and 33,510 were expressed in the roots and leaves, respectively. Biological pathways and candidate genes involved in selenium tolerance mechanisms were identified. Differential expression analysis identified 25 genes located in four pathways that were significantly responsive to selenite in C. hupingshanensis seedlings. The results of RNA sequencing (RNA-Seq) and quantitative real-time PCR (RT-qPCR) confirmed that storage function, oxidation, transamination and selenation play very important roles in the selenium tolerance in C. hupingshanensis. Furthermore, a different degradation pathway synthesizing malformed or deformed selenoproteins increased selenium tolerance at different selenite concentrations. This study provides novel insights into the mechanisms of selenium tolerance in a hyperaccumulator plant, and should serve as a rich gene resource for C. hupingshanensis.
Collapse
Affiliation(s)
- Yifeng Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.,Key Laboratory of Biological Resources Protection and Utilization of Hubei Province, Hubei University for Nationalities, Enshi, 44500, China.,Collage of Biological Science and Technology, Hubei University for Nationalities, Enshi, 44500, China
| | - Qiaoyu Tang
- Key Laboratory of Biological Resources Protection and Utilization of Hubei Province, Hubei University for Nationalities, Enshi, 44500, China
| | - Meiru Wu
- Key Laboratory of Biological Resources Protection and Utilization of Hubei Province, Hubei University for Nationalities, Enshi, 44500, China
| | - Di Mou
- Key Laboratory of Biological Resources Protection and Utilization of Hubei Province, Hubei University for Nationalities, Enshi, 44500, China
| | - Hui Liu
- Collage of Biological Science and Technology, Hubei University for Nationalities, Enshi, 44500, China
| | - Shouchuang Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Chi Zhang
- Collage of Biological Science and Technology, Hubei University for Nationalities, Enshi, 44500, China
| | - Li Ding
- Collage of Biological Science and Technology, Hubei University for Nationalities, Enshi, 44500, China
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
111
|
Lu X, Zhang X, Duan H, Lian C, Liu C, Yin W, Xia X. Three stress-responsive NAC transcription factors from Populus euphratica differentially regulate salt and drought tolerance in transgenic plants. PHYSIOLOGIA PLANTARUM 2018; 162:73-97. [PMID: 28776695 DOI: 10.1111/ppl.12613] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 07/04/2017] [Accepted: 07/10/2017] [Indexed: 05/04/2023]
Abstract
Stress-responsive NAM, Arabidopsis transcription activation factor 1/2 (ATAF1/2) and CUC2 (SNAC) genes are being used to alter stress tolerance in Arabidopsis or grasses through genetic engineering. However, limited reports are available about the functional characteristics of SNAC in trees. In this study, three putative NAC proteins were identified from Populus euphratica. PeNAC034 and PeNAC045 were classified into the ATAF subgroup and PeNAC036 into the ANAC072 subgroup. These three SNAC transcription factors were localized in the nucleus and contained the transcription activation domain in their C-terminal. Under drought and salt stresses, PeNAC036 was strongly induced in the whole plant, but PeNAC034 was significantly suppressed in the roots and stems, and PeNAC045 was inhibited in the roots. PeNAC036 overexpression in Arabidopsis wild-type (WT) (OEPeNAC036) and PeNAC036 complementation in mutant anac072 (anac072/PeNAC036) lines increased tolerance to salt and drought, whereas PeNAC034 overexpression in WT (OEPeNAC034) and PeNAC034 complementation in mutant ataf1 (ataf1/PeNAC034) lines enhanced salt and drought sensitivity. After drought and salt treatments, the expression levels of COR47, RD29B, ERD11, RD22 and DREB2A were upregulated in OEPeNAC036 and anac072/PeNAC036 lines, but were downregulated in OEPeNAC034 and ataf1/PeNAC034 plants. Compared with WT and Vector lines, PeNAC045 overexpression in poplar WT (OEPeNAC045) led to a significant decrease in the net photosynthesis rate, stomatal conductance and transpiration rate under salinity and drought conditions. These results suggest that P. euphratica can adapt to the environment of high salinity and drought, which may be related to the differential expression patterns of SNAC genes.
Collapse
Affiliation(s)
- Xin Lu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, P. R. China
| | - Xiaofei Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, P. R. China
| | - Hui Duan
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, P. R. China
| | - Conglong Lian
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, P. R. China
| | - Chao Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, P. R. China
| | - Weilun Yin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, P. R. China
| | - Xinli Xia
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, P. R. China
| |
Collapse
|
112
|
Yang F, Ding X, Chen J, Shen Y, Kong L, Li N, Chu Z. Functional analysis of the GRMZM2G174449 promoter to identify Rhizoctonia solani-inducible cis-elements in maize. BMC PLANT BIOLOGY 2017; 17:233. [PMID: 29202693 PMCID: PMC5715495 DOI: 10.1186/s12870-017-1181-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 11/22/2017] [Indexed: 05/27/2023]
Abstract
BACKGROUND Banded leaf and sheath blight (BLSB), caused by the necrotrophic fungus Rhizoctonia solani, is a highly devastating disease in most maize and rice growing areas of the world. However, the molecular mechanisms of perceiving pathogen signals are poorly understood in hosts. RESULTS Here, we identified a Rhizoctonia solani-inducible promoter pGRMZM2G174449 in maize. Deletion analysis showed that the -574 to -455 fragment was necessary for pGRMZM2G174449 in responding to R. solani and this fragment contained the unknown pathogen-inducible cis-elements according to the bioinformatics analysis. Furthermore, detailed quantitative assays showed that two cis-elements, GCTGA in the -567 to -563 region and TATAT in the -485 to -481 region, were specifically responsible for the R. solani-inducible activity. A series of point mutation analysis indicated that the two cis-elements have the conserved motifs of NHWGN and DWYWT, respectively. CONCLUSION Our results indicated that pGRMZM2G174449 is a good R. solani-inducible promoter suitable for genetic engineering of BLSB resistance. And NHWGN and DWYWT are two R. solani-inducible cis-elements that play important roles in pGRMZM2G174449 responding to R. solani.
Collapse
Affiliation(s)
- Fangfang Yang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai an, 271018 Shandong Province People’s Republic of China
| | - Xinhua Ding
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai an, 271018 Shandong Province People’s Republic of China
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai an, 271018 Shandong Province People’s Republic of China
| | - Jing Chen
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai an, 271018 Shandong Province People’s Republic of China
| | - Yanting Shen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai an, 271018 Shandong Province People’s Republic of China
| | - Lingguang Kong
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai an, 271018 Shandong Province People’s Republic of China
| | - Ning Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai an, 271018 Shandong Province People’s Republic of China
| | - Zhaohui Chu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai an, 271018 Shandong Province People’s Republic of China
| |
Collapse
|
113
|
Singh D, Kumar D, Satapathy L, Pathak J, Chandra S, Riaz A, Bhaganagre G, Dhariwal R, Kumar M, Prabhu KV, Balyan HS, Gupta PK, Mukhopadhyay K. Insights of Lr28 mediated wheat leaf rust resistance: Transcriptomic approach. Gene 2017; 637:72-89. [DOI: 10.1016/j.gene.2017.09.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/31/2017] [Accepted: 09/14/2017] [Indexed: 01/09/2023]
|
114
|
Genome-wide identification and expression analysis of transcription factors in Solanum lycopersicum. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.aggene.2017.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
115
|
Tandon G, Singh S, Kaur S, Sarika, Iquebal MA, Rai A, Kumar D. Computational deciphering of biotic stress associated genes in tomato ( Solanum lycopersicum). GENOMICS DATA 2017; 14:82-90. [PMID: 29062693 PMCID: PMC5643083 DOI: 10.1016/j.gdata.2017.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 09/20/2017] [Accepted: 09/23/2017] [Indexed: 01/17/2023]
Abstract
Tomato (Solanum lycopersicum) is one of the major vegetable plant and a model system for fruit development. Its global importance is due to its lycopene pigment which has anti-oxidative and anti-cancerous properties. Though > 1.5 M biotic stress associated ESTs of tomato are available but cumulative analysis to predict genes is warranted. Availability of whole genome de novo assembly can advantageously be used to map them over different chromosome. Further, available 0.14 M catalogued markers can be used to introgress specific desirable genes in varietal improvement program. We report here 57 novel genes associated with biotic stress of tomato along with 50 genes having physical location over different chromosomes. We also report 52 cis-regulating elements and 69 putative miRNAs which are involved in regulation of these biotic stresses associated genes. These putative candidate genes associated with biotic stress can be used in molecular breeding in the endeavor of tomato productivity along with its sustainable germplasm management. ESts related to biotic stress were collected and assembled into contigs. Total 57 novel genes were computationally mined from the assembled contigs. Among the predicted novel gene, 50 genes were mapped on tomato genome. 52 cis-regulating elements and 69 putative miRNAs were predicted for the novel genes.
Collapse
Affiliation(s)
- G Tandon
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 1100 12, India.,Departments of Computational Biology & Bioinformatics, Jacob School of Biotechnology & Bio-Engineering, SHUATS, Allahabad 211007, India
| | - S Singh
- Departments of Computational Biology & Bioinformatics, Jacob School of Biotechnology & Bio-Engineering, SHUATS, Allahabad 211007, India
| | - S Kaur
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 1100 12, India.,Departments of Computational Biology & Bioinformatics, Jacob School of Biotechnology & Bio-Engineering, SHUATS, Allahabad 211007, India
| | - Sarika
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 1100 12, India
| | - M A Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 1100 12, India
| | - A Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 1100 12, India
| | - D Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 1100 12, India
| |
Collapse
|
116
|
Ezer D, Shepherd SJK, Brestovitsky A, Dickinson P, Cortijo S, Charoensawan V, Box MS, Biswas S, Jaeger KE, Wigge PA. The G-Box Transcriptional Regulatory Code in Arabidopsis. PLANT PHYSIOLOGY 2017; 175:628-640. [PMID: 28864470 PMCID: PMC5619884 DOI: 10.1104/pp.17.01086] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 08/30/2017] [Indexed: 05/19/2023]
Abstract
Plants have significantly more transcription factor (TF) families than animals and fungi, and plant TF families tend to contain more genes; these expansions are linked to adaptation to environmental stressors. Many TF family members bind to similar or identical sequence motifs, such as G-boxes (CACGTG), so it is difficult to predict regulatory relationships. We determined that the flanking sequences near G-boxes help determine in vitro specificity but that this is insufficient to predict the transcription pattern of genes near G-boxes. Therefore, we constructed a gene regulatory network that identifies the set of bZIPs and bHLHs that are most predictive of the expression of genes downstream of perfect G-boxes. This network accurately predicts transcriptional patterns and reconstructs known regulatory subnetworks. Finally, we present Ara-BOX-cis (araboxcis.org), a Web site that provides interactive visualizations of the G-box regulatory network, a useful resource for generating predictions for gene regulatory relations.
Collapse
Affiliation(s)
- Daphne Ezer
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Samuel J K Shepherd
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Anna Brestovitsky
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Patrick Dickinson
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Sandra Cortijo
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Varodom Charoensawan
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
- Department of Biochemistry, Faculty of Science, and Integrative Computational BioScience Center, Mahidol University, Bangkok 10400, Thailand
| | - Mathew S Box
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Surojit Biswas
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Katja E Jaeger
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Philip A Wigge
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| |
Collapse
|
117
|
Noman A, Liu Z, Aqeel M, Zainab M, Khan MI, Hussain A, Ashraf MF, Li X, Weng Y, He S. Basic leucine zipper domain transcription factors: the vanguards in plant immunity. Biotechnol Lett 2017; 39:1779-1791. [DOI: 10.1007/s10529-017-2431-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/31/2017] [Indexed: 01/05/2023]
|
118
|
Zha L, Liu S, Liu J, Jiang C, Yu S, Yuan Y, Yang J, Wang Y, Huang L. DNA Methylation Influences Chlorogenic Acid Biosynthesis in Lonicera japonica by Mediating LjbZIP8 to Regulate Phenylalanine Ammonia-Lyase 2 Expression. FRONTIERS IN PLANT SCIENCE 2017; 8:1178. [PMID: 28740500 PMCID: PMC5502268 DOI: 10.3389/fpls.2017.01178] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 06/20/2017] [Indexed: 05/10/2023]
Abstract
The content of active compounds differ in buds and flowers of Lonicera japonica (FLJ) and L. japonica var. chinensis (rFLJ). Chlorogenic acid (CGAs) were major active compounds of L. japonica and regarded as measurements for quality evaluation. However, little is known concerning the formation of active compounds at the molecular level. We quantified the major CGAs in FLJ and rFLJ, and found the concentrations of CGAs were higher in the buds of rFLJ than those of FLJ. Further analysis of CpG methylation of CGAs biosynthesis genes showed differences between FLJ and rFLJ in the 5'-UTR of phenylalanine ammonia-lyase 2 (PAL2). We identified 11 LjbZIP proteins and 24 rLjbZIP proteins with conserved basic leucine zipper domains, subcellular localization, and electrophoretic mobility shift assay showed that the transcription factor LjbZIP8 is a nuclear-localized protein that specifically binds to the G-box element of the LjPAL2 5'-UTR. Additionally, a transactivation assay and LjbZIP8 overexpression in transgenic tobacco indicated that LjbZIP8 could function as a repressor of transcription. Finally, treatment with 5-azacytidine decreased the transcription level of LjPAL2 and CGAs content in FLJ leaves. These results raise the possibility that DNA methylation might influence the recruitment of LjbZIP8, regulating PAL2 expression level and CGAs content in L. japonica.
Collapse
Affiliation(s)
- Liangping Zha
- College of Pharmacy, Anhui University of Chinese MedicineHefei, China
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese MedicineHefei, China
| | - Shuang Liu
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
- School of Chinese Materia Medica, Beijing University of Chinese MedicineBeijing, China
| | - Juan Liu
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Chao Jiang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Shulin Yu
- College of Pharmacy, Anhui University of Chinese MedicineHefei, China
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Yuan Yuan
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Jian Yang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Yaolong Wang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Luqi Huang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| |
Collapse
|
119
|
Castro PH, Lilay GH, Muñoz-Mérida A, Schjoerring JK, Azevedo H, Assunção AGL. Phylogenetic analysis of F-bZIP transcription factors indicates conservation of the zinc deficiency response across land plants. Sci Rep 2017. [PMID: 28630437 PMCID: PMC5476651 DOI: 10.1038/s41598-017-03903-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Basic leucine zipper (bZIP) transcription factors control important developmental and physiological processes in plants. In Arabidopsis thaliana, the three gene F-bZIP subfamily has been associated with zinc deficiency and salt stress response. Benefiting from the present abundance of plant genomic data, we performed an evolutionary and structural characterization of plant F-bZIPs. We observed divergence during seed plant evolution, into two groups and inferred different selective pressures for each. Group 1 contains AtbZIP19 and AtbZIP23 and appears more conserved, whereas Group 2, containing AtbZIP24, is more prone to gene loss and expansion events. Transcriptomic and experimental data reinforced AtbZIP19/23 as pivotal regulators of the zinc deficiency response, mostly via the activation of genes from the ZIP metal transporter family, and revealed that they are the main regulatory switch of AtZIP4. A survey of AtZIP4 orthologs promoters across different plant taxa revealed an enrichment of the Zinc Deficiency Response Element (ZDRE) to which both AtbZIP19/23 bind. Overall, our results indicate that while the AtbZIP24 function in the regulation of the salt stress response may be the result of neo-functionalization, the AtbZIP19/23 function in the regulation of the zinc deficiency response may be conserved in land plants (Embryophytes).
Collapse
Affiliation(s)
- Pedro Humberto Castro
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Copenhagen, Denmark
| | - Grmay H Lilay
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Copenhagen, Denmark
| | - Antonio Muñoz-Mérida
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, University of Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Jan K Schjoerring
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Copenhagen, Denmark
| | - Herlânder Azevedo
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, University of Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua Campo Alegre, 4169-007, Porto, Portugal
| | - Ana G L Assunção
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Copenhagen, Denmark. .,CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, University of Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.
| |
Collapse
|
120
|
Silvia Sebastiani M, Bagnaresi P, Sestili S, Biselli C, Zechini A, Orrù L, Cattivelli L, Ficcadenti N. Transcriptome Analysis of the Melon- Fusarium oxysporum f. sp. melonis Race 1.2 Pathosystem in Susceptible and Resistant Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:362. [PMID: 28367157 PMCID: PMC5356040 DOI: 10.3389/fpls.2017.00362] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Accepted: 03/01/2017] [Indexed: 05/20/2023]
Abstract
Fusarium oxysporum f. sp. melonis Snyd. & Hans race 1.2 (FOM1.2) is the most virulent and yield-limiting pathogen of melon (Cucumis melo L.) worldwide. Current information suggest that the resistance to race 1.2 is controlled by multiple recessive genes and strongly affected by the environment. RNA-Seq analysis was used to identify candidate resistance genes and to dissect the early molecular processes deployed during melon-FOM1.2 interaction in the resistant doubled haploid line NAD and in the susceptible genotype Charentais-T (CHT) at 24 and 48 h post-inoculation (hpi). The transcriptome analysis of the NAD-FOM1.2 interaction identified 2,461 and 821 differentially expressed genes (DEGs) at 24 hpi and at 48 hpi, respectively, while in susceptible combination CHT-FOM1.2, 882 and 2,237 DEGs were recovered at 24 hpi and at 48 hpi, respectively. The overall expression profile suggests a prompt activation of the defense responses in NAD due to its basal defense-related machinery that allows an early pathogen recognition. Gene Ontology (GO) enrichment analyses revealed a total of 57 GO terms shared by both genotypes and consistent with response to fungal infection. GO classes named "chitinase activity," "cellulase activity," "defense response, incompatible interaction," "auxin polar transport" emerged as major factors of resistance to FOM1.2. The data indicated that NAD reacts to FOM1.2 with a fine regulation of Ca2+-mediated signaling pathways, cell wall reorganization, and hormone crosstalk (jasmonate and ethylene, auxin and abscissic acid). Several unannotated transcripts were recovered providing a basis for a further exploration of the melon resistance genes. DEGs belonging to the FOM1.2 genome were also detected in planta as a resource for the identification of potential pathogenicity factors. This work provides a broader view of the dynamic changes of the melon transcriptome triggered by FOM1.2 and highlights that the resistance response of NAD is mainly signaled by jasmonic acid and ethylene pathways mediated by ABA and auxin. The role of candidate plant and fungal responsive genes involved in the resistance is discussed.
Collapse
Affiliation(s)
- M. Silvia Sebastiani
- Research Unit for Vegetable Crops in Central Areas, Council for Agricultural Research and EconomicsAscoli Piceno, Italy
| | - Paolo Bagnaresi
- Genomics Research Centre, Council for Agricultural Research and EconomicsPiacenza, Italy
| | - Sara Sestili
- Research Unit for Vegetable Crops in Central Areas, Council for Agricultural Research and EconomicsAscoli Piceno, Italy
| | - Chiara Biselli
- Genomics Research Centre, Council for Agricultural Research and EconomicsPiacenza, Italy
| | - Antonella Zechini
- Genomics Research Centre, Council for Agricultural Research and EconomicsPiacenza, Italy
| | - Luigi Orrù
- Genomics Research Centre, Council for Agricultural Research and EconomicsPiacenza, Italy
| | - Luigi Cattivelli
- Genomics Research Centre, Council for Agricultural Research and EconomicsPiacenza, Italy
| | - Nadia Ficcadenti
- Research Unit for Vegetable Crops in Central Areas, Council for Agricultural Research and EconomicsAscoli Piceno, Italy
| |
Collapse
|
121
|
Yang F, Li W, Jiang N, Yu H, Morohashi K, Ouma WZ, Morales-Mantilla DE, Gomez-Cano FA, Mukundi E, Prada-Salcedo LD, Velazquez RA, Valentin J, Mejía-Guerra MK, Gray J, Doseff AI, Grotewold E. A Maize Gene Regulatory Network for Phenolic Metabolism. MOLECULAR PLANT 2017; 10:498-515. [PMID: 27871810 DOI: 10.1016/j.molp.2016.10.020] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/20/2016] [Accepted: 10/31/2016] [Indexed: 05/23/2023]
Abstract
The translation of the genotype into phenotype, represented for example by the expression of genes encoding enzymes required for the biosynthesis of phytochemicals that are important for interaction of plants with the environment, is largely carried out by transcription factors (TFs) that recognize specific cis-regulatory elements in the genes that they control. TFs and their target genes are organized in gene regulatory networks (GRNs), and thus uncovering GRN architecture presents an important biological challenge necessary to explain gene regulation. Linking TFs to the genes they control, central to understanding GRNs, can be carried out using gene- or TF-centered approaches. In this study, we employed a gene-centered approach utilizing the yeast one-hybrid assay to generate a network of protein-DNA interactions that participate in the transcriptional control of genes involved in the biosynthesis of maize phenolic compounds including general phenylpropanoids, lignins, and flavonoids. We identified 1100 protein-DNA interactions involving 54 phenolic gene promoters and 568 TFs. A set of 11 TFs recognized 10 or more promoters, suggesting a role in coordinating pathway gene expression. The integration of the gene-centered network with information derived from TF-centered approaches provides a foundation for a phenolics GRN characterized by interlaced feed-forward loops that link developmental regulators with biosynthetic genes.
Collapse
Affiliation(s)
- Fan Yang
- Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Wei Li
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Nan Jiang
- Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Haidong Yu
- Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Kengo Morohashi
- Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Wilberforce Zachary Ouma
- Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Molecular, Cellular, and Developmental Biology (MCDB) Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Daniel E Morales-Mantilla
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA; Success in Graduate Education (SiGuE) Program, The Ohio State University, Columbus, OH 43210, USA
| | - Fabio Andres Gomez-Cano
- Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Eric Mukundi
- Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Luis Daniel Prada-Salcedo
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Roberto Alers Velazquez
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA; Success in Graduate Education (SiGuE) Program, The Ohio State University, Columbus, OH 43210, USA
| | - Jasmin Valentin
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA; Success in Graduate Education (SiGuE) Program, The Ohio State University, Columbus, OH 43210, USA
| | - Maria Katherine Mejía-Guerra
- Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - John Gray
- Department of Biological Sciences, University of Toledo, Toledo, OH 43560, USA
| | - Andrea I Doseff
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Department of Physiology and Cell Biology, Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Erich Grotewold
- Center for Applied Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA.
| |
Collapse
|
122
|
Li N, Chen J, Yang F, Wei S, Kong L, Ding X, Chu Z. Identification of two novel Rhizoctonia solani-inducible cis-acting elements in the promoter of the maize gene, GRMZM2G315431. Sci Rep 2017; 7:42059. [PMID: 28163300 PMCID: PMC5292686 DOI: 10.1038/srep42059] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 01/06/2017] [Indexed: 01/12/2023] Open
Abstract
Plants are continuously exposed to myriad pathogen stresses. However, the molecular mechanisms by which these stress signals are perceived and transduced are poorly understood. In this study, the maize gene GRMZM2G315431 was identified to be highly inducible by Rhizoctonia solani infection, suggesting that the promoter of GRMZM2G315431 (pGRMZM2G315431) might contain a specific cis-acting element responsive to R. solani attack. To identify the R. solani-responsive element in pGRMZM2G315431, a series of binary plant transformation vectors were constructed by fusing pGRMZM2G315431 or its deletion-derivatives with the reporter genes. In the transient gene expression system of Nicotiana benthamiana leaves inoculated with R. solani, GUS quantification suggested that the DNA fragment contains the unknown pathogen-inducible cis-elements in the -1323 to -1212 region. Furthermore, detailed quantitative assays showed that two novel cis-elements, GTTGA in the -1243 to -1239 region and TATTT in the -1232 to -1228 region, were responsible for the R. solani-inducible activity. These two cis-elements were also identified to have R. solani-specific-inducible activity in stable transgenic rice plants, suggesting the existence of a novel regulation mechanism involved in the interaction between R. solani and Zea mays.
Collapse
Affiliation(s)
- Ning Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018, Shandong, PR China
| | - Jing Chen
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018, Shandong, PR China
| | - Fangfang Yang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018, Shandong, PR China
| | - Shutong Wei
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018, Shandong, PR China
| | - Lingguang Kong
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018, Shandong, PR China
| | - Xinhua Ding
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018, Shandong, PR China
| | - Zhaohui Chu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018, Shandong, PR China
| |
Collapse
|
123
|
Dash M, Yordanov YS, Georgieva T, Tschaplinski TJ, Yordanova E, Busov V. Poplar PtabZIP1-like enhances lateral root formation and biomass growth under drought stress. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:692-705. [PMID: 27813246 DOI: 10.1111/tpj.13413] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 10/18/2016] [Accepted: 10/27/2016] [Indexed: 05/07/2023]
Abstract
Developing drought-resistance varieties is a major goal for bioenergy crops, such as poplar (Populus), which will be grown on marginal lands with little or no water input. Root architecture can affect drought resistance, but few genes that affect root architecture in relation to water availability have been identified. Here, using activation tagging in the prime bioenergy crop poplar, we have identified a mutant that overcomes the block of lateral root (LR) formation under osmotic stress. Positioning of the tag, validation of the activation and recapitulation showed that the phenotype is caused by the poplar PtabZIP1-like (PtabZIP1L) gene with highest homology to bZIP1 from Arabidopsis. PtabZIP1L is predominantly expressed in roots, particularly in zones where lateral root primordia (LRP) initiate and LR differentiate and emerge. Transgenics overexpressing PtabZIP1L showed precocious LRP and LR development, while PtabZIP1L suppression significantly delayed both LRP and LR formation. Transgenic overexpression and suppression of PtabZIP1L also resulted in modulation of key metabolites like proline, asparagine, valine and several flavonoids. Consistently, expression of both of the poplar Proline Dehydrogenase orthologs and two of the Flavonol Synthases genes was also increased and decreased in overexpressed and suppressed transgenics, respectively. These findings suggest that PtabZIP1L mediates LR development and drought resistance through modulation of multiple metabolic pathways.
Collapse
Affiliation(s)
- Madhumita Dash
- Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Yordan S Yordanov
- Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Tatyana Georgieva
- Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | | | - Elena Yordanova
- Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Victor Busov
- Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| |
Collapse
|
124
|
Sharma I, Kaur N, Pati PK. Brassinosteroids: A Promising Option in Deciphering Remedial Strategies for Abiotic Stress Tolerance in Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:2151. [PMID: 29326745 PMCID: PMC5742319 DOI: 10.3389/fpls.2017.02151] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 12/05/2017] [Indexed: 05/03/2023]
Abstract
Rice is an important staple crop as it feeds about a half of the earth's population. It is known to be sensitive to a range of abiotic stresses which result in significant decline in crop productivity. Recently, the use of phytohormones for abiotic stress amelioration has generated considerable interest. Plants adapt to various environmental stresses by undergoing series of changes at physiological and molecular levels which are cooperatively modulated by various phytohormones. Brassinosteroids (BRs) are a class of naturally occurring steroidal phytohormones, best known for their role in plant growth and development. For the past two decades, greater emphasis on studies related to BRs biosynthesis, distribution and signaling has resulted in better understanding of BRs function. Recent advances in the use of contemporary genetic, biochemical and proteomic tools, with a vast array of accessible biological resources has led to an extensive exploration of the key regulatory components in BR signaling networks, thus making it one of the most well-studied hormonal pathways in plants. The present review highlights the advancements of knowledge in BR research and links it with its growing potential in abiotic stress management for important crop like rice.
Collapse
|
125
|
Li X, Fan S, Hu W, Liu G, Wei Y, He C, Shi H. Two Cassava Basic Leucine Zipper (bZIP) Transcription Factors (MebZIP3 and MebZIP5) Confer Disease Resistance against Cassava Bacterial Blight. FRONTIERS IN PLANT SCIENCE 2017; 8:2110. [PMID: 29276527 PMCID: PMC5727076 DOI: 10.3389/fpls.2017.02110] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 11/27/2017] [Indexed: 05/19/2023]
Abstract
Basic domain-leucine zipper (bZIP) transcription factor, one type of conserved gene family, plays an important role in plant development and stress responses. Although 77 MebZIPs have been genome-wide identified in cassava, their in vivo roles remain unknown. In this study, we analyzed the expression pattern and the function of two MebZIPs (MebZIP3 and MebZIP5) in response to pathogen infection. Gene expression analysis indicated that MebZIP3 and MebZIP5 were commonly regulated by flg22, Xanthomonas axonopodis pv. manihotis (Xam), salicylic acid (SA), and hydrogen peroxide (H2O2). Subcellular localization analysis showed that MebZIP3 and MebZIP5 are specifically located in cell nucleus. Through overexpression in tobacco, we found that MebZIP3 and MebZIP5 conferred improved disease resistance against cassava bacterial blight, with more callose depositions. On the contrary, MebZIP3- and MebZIP5-silenced plants by virus-induced gene silencing (VIGS) showed disease sensitive phenotype, lower transcript levels of defense-related genes and less callose depositions. Taken together, this study highlights the positive role of MebZIP3 and MebZIP5 in disease resistance against cassava bacterial blight for further utilization in genetic improvement of cassava disease resistance.
Collapse
Affiliation(s)
- Xiaolin Li
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Shuhong Fan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Guoyin Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Yunxie Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Chaozu He
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
- *Correspondence: Haitao Shi, Chaozu He,
| | - Haitao Shi
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources and College of Biology, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
- *Correspondence: Haitao Shi, Chaozu He,
| |
Collapse
|
126
|
Matros A, Liu G, Hartmann A, Jiang Y, Zhao Y, Wang H, Ebmeyer E, Korzun V, Schachschneider R, Kazman E, Schacht J, Longin F, Reif JC, Mock HP. Genome-metabolite associations revealed low heritability, high genetic complexity, and causal relations for leaf metabolites in winter wheat (Triticum aestivum). JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:415-428. [PMID: 28007948 PMCID: PMC5441906 DOI: 10.1093/jxb/erw441] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
We investigated associations between the metabolic phenotype, consisting of quantitative data of 76 metabolites from 135 contrasting winter wheat (Triticum aestivum) lines, and 17 372 single nucleotide polymorphism (SNP) markers. Metabolite profiles were generated from flag leaves of plants from three different environments, with average repeatabilities of 0.5-0.6. The average heritability of 0.25 was unaffected by the heading date. Correlations among metabolites reflected their functional grouping, highlighting the strict coordination of various routes of the citric acid cycle. Genome-wide association studies identified significant associations for six metabolic traits, namely oxalic acid, ornithine, L-arginine, pentose alcohol III, L-tyrosine, and a sugar oligomer (oligo II), with between one and 17 associated SNPs. Notable associations with genes regulating transcription or translation explained between 2.8% and 32.5% of the genotypic variance (pG). Further candidate genes comprised metabolite carriers (pG 32.5-38.1%), regulatory proteins (pG 0.3-11.1%), and metabolic enzymes (pG 2.5-32.5%). The combinatorial use of genomic and metabolic data to construct partially directed networks revealed causal inferences in the correlated metabolite traits and associated SNPs. The evaluated causal relationships will provide a basis for predicting the effects of genetic interferences on groups of correlated metabolic traits, and thus on specific metabolic phenotypes.
Collapse
Affiliation(s)
- Andrea Matros
- Department of Physiology and Cell Biology, Applied Biochemistry, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Guozheng Liu
- Department of Breeding Research, Quantitative Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Anja Hartmann
- Department of Physiology and Cell Biology, Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Yong Jiang
- Department of Breeding Research, Quantitative Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Yusheng Zhao
- Department of Breeding Research, Quantitative Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Huange Wang
- Biometris, Department of Plant Sciences, Wageningen University, PB Wageningen, The Netherlands
| | | | | | | | - Ebrahim Kazman
- Lantmännen SW Seed Hadmersleben GmbH, Hadmersleben, Germany
| | | | - Friedrich Longin
- University of Hohenheim, State Plant Breeding Institute, Stuttgart, Germany
| | - Jochen Christoph Reif
- Department of Breeding Research, Quantitative Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Hans-Peter Mock
- Department of Physiology and Cell Biology, Applied Biochemistry, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| |
Collapse
|
127
|
Gupta P, Nutan KK, Singla-Pareek SL, Pareek A. Abiotic Stresses Cause Differential Regulation of Alternative Splice Forms of GATA Transcription Factor in Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:1944. [PMID: 29181013 PMCID: PMC5693882 DOI: 10.3389/fpls.2017.01944] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 10/30/2017] [Indexed: 05/05/2023]
Abstract
The GATA gene family is one of the most conserved families of transcription factors, playing a significant role in different aspects of cellular processes, in organisms ranging from fungi to angiosperms. GATA transcription factors are DNA-binding proteins, having a class IV zinc-finger motif CX2CX17-20CX2C followed by a highly basic region and are known to bind a consensus sequence WGATAR. In plants, GATAs are known to be involved in light-dependent gene regulation and nitrate assimilation. However, a comprehensive analysis of these GATA gene members has not yet been highlighted in rice when subjected to environmental stresses. In this study, we present an overview of the GATA gene family in rice (OsGATA) in terms of, their chromosomal distribution, domain architecture, and phylogeny. Our study has revealed the presence of 28 genes, encoding 35 putative GATA transcription factors belonging to seven subfamilies in the rice genome. Transcript abundance analysis in contrasting genotypes of rice-IR64 (salt sensitive) and Pokkali (salt tolerant), for individual GATA members indicated their differential expression in response to various abiotic stresses such as salinity, drought, and exogenous ABA. One of the members of subfamily VII-OsGATA23a, emerged as a multi-stress responsive transcription factor giving elevated expression levels in response to salinity and drought. ABA also induces expression of OsGATA23a by 35 and 55-folds in IR64 and Pokkali respectively. However, OsGATA23b, an alternative splice variant of OsGATA23 did not respond to above-mentioned stresses. Developmental regulation of the OsGATA genes based on a publicly available microarray database showed distinct expression patterns for most of the GATA members throughout different stages of rice development. Altogether, our results suggest inherent roles of diverse OsGATA factors in abiotic stress signaling and also throw some light on the tight regulation of the spliced variants of OsGATA genes in response to different environmental conditions.
Collapse
Affiliation(s)
- Priyanka Gupta
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Kamlesh K. Nutan
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sneh L. Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- *Correspondence: Ashwani Pareek
| |
Collapse
|
128
|
Kumar P, Jaiswal V, Pal T, Singh J, Chauhan RS. Comparative whole-transcriptome analysis in Podophyllum species identifies key transcription factors contributing to biosynthesis of podophyllotoxin in P. hexandrum. PROTOPLASMA 2017; 254:217-228. [PMID: 26733390 DOI: 10.1007/s00709-015-0938-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 12/21/2015] [Indexed: 06/05/2023]
Abstract
Podophyllum species (Podophyllum hexandrum Royle and Podophyllum peltatum) are a major source of deriving anticancer drugs from their major chemical constituent, podophyllotoxin. However, information lacks on regulatory components of podophyllotoxin biosynthesis; therefore, different classes of transcription factors were identified through mining transcriptomes of Podophyllum species and validated through qRT-PCR analysis vis-à-vis podophyllotoxin contents in different tissues/organs of Podophyllum hexandrum. A total of 82, 278, 70, and 90 transcripts were identified in shoots and 89, 273, 72, and 91 transcripts in rhizomes of P. hexandrum transcriptome; 70, 268, 48, and 92 transcripts were in shoots and 58, 245, 41, and 85 transcripts in rhizomes of P. peltatum transcriptome corresponding to bZIP, MYB, WRKY, and bHLH families of transcription factors, which have been shown in regulating biosynthesis of secondary metabolites. Two unique transcripts encoding bHLH and MYB/SANT TFs in shoots of P. peltatum (medp_podpe_41091 and medp_podpe_2547) and bZIP and MYB TFs in rhizomes of P. hexandrum (medp_podhe_163581 and medp_podhe_147614) correlated with podophyllotoxin content. Quantification of podophyllotoxin and comparative expression analysis between high (2.51 %) versus low (0.59) podophyllotoxin content accessions revealed 0.04 to ~16-folds increase in transcripts of transcription factors, thereby further supporting the association of identified transcription factors with podophyllotoxin content. bZIP TF showed the highest transcript abundance (19.60-folds) in P. hexandrum rhizomes (2.51 % podophyllotoxin) compared to shoots (0.01 %). In silico analysis of putative promoter regions of pathway genes in other plant species revealed the presence of sequence elements for MYB and WRKY transcription factors, thereby suggesting their role in controlling the production of podophyllotoxin. A repertoire of additional transcription factors has been provided, which can be functionally validated and used in designing a suitable genetic intervention strategy towards enhanced production of podophyllotoxin.
Collapse
Affiliation(s)
- Pawan Kumar
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, 173234, Solan, Himachal Pradesh, India
| | - Varun Jaiswal
- Department of Computer Science and Bioinformatics, Shoolini University, Solan, 173212, Himachal Pradesh, India
| | - Tarun Pal
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, 173234, Solan, Himachal Pradesh, India
| | - Jagdish Singh
- Agroforestry and Extension Division, Himalayan Forest Research Institute, Panthaghati, 171009, Shimla, Himachal Pradesh, India
| | - Rajinder S Chauhan
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, 173234, Solan, Himachal Pradesh, India.
| |
Collapse
|
129
|
Long N, Ren X, Xiang Z, Wan W, Dong Y. Sequencing and characterization of leaf transcriptomes of six diploid Nicotiana species. JOURNAL OF BIOLOGICAL RESEARCH (THESSALONIKE, GREECE) 2016; 23:6. [PMID: 27096138 PMCID: PMC4835900 DOI: 10.1186/s40709-016-0048-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 04/05/2016] [Indexed: 11/19/2022]
Abstract
BACKGROUND Nicotiana belongs to the Solanaceae family that includes important crops such as tomato, potato, eggplant, and pepper. Nicotiana species are of worldwide economic importance and are important model plants for scientific research. Here we present the comparative analysis of the transcriptomes of six wild diploid Nicotiana species. Wild relatives provide an excellent study system for the analysis of the genetic basis for various traits, especially disease resistance. RESULTS Whole transcriptome sequencing (RNA-seq) was performed for leaves of six diploid Nicotiana species, i.e. Nicotiana glauca, Nicotiana noctiflora, Nicotiana cordifolia, Nicotiana knightiana, Nicotiana setchellii and Nicotiana tomentosiformis. For each species, 9.0-22.3 Gb high-quality clean data were generated, and 67,073-182,046 transcripts were assembled with lengths greater than 100 bp. Over 90 % of the ORFs in each species had significant similarity with proteins in the NCBI non-redundant protein sequence (NR) database. A total of 2491 homologs were identified and used to construct a phylogenetic tree from the respective transcriptomes in Nicotiana. Bioinformatic analysis identified resistance gene analogs, major transcription factor families, and alkaloid transporter genes linked to plant defense. CONCLUSIONS This is the first report on the leaf transcriptomes of six wild Nicotiana species by Illumina paired-end sequencing and de novo assembly without a reference genome. These sequence resources hopefully will provide an opportunity for identifying genes involved in plant defense and several important quality traits in wild Nicotiana and will accelerate functional genomic studies and genetic improvement efforts of Nicotiana or other important Solanaceae crops in the future.
Collapse
Affiliation(s)
- Ni Long
- />Faculty of Life Science and Technology, Kunming University of Science and Technology, South Jingming Road No.727, Kunming, 650500 Yunnan China
| | - Xueliang Ren
- />Guizhou Tobacco Research Institute, North Yuntan Road, Jinyang District, Guiyang, 550003 Guizhou China
| | - Zhidan Xiang
- />State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiaochang Road, Kunming, 650223 Yunnan China
| | - Wenting Wan
- />Faculty of Life Science and Technology, Kunming University of Science and Technology, South Jingming Road No.727, Kunming, 650500 Yunnan China
| | - Yang Dong
- />Faculty of Life Science and Technology, Kunming University of Science and Technology, South Jingming Road No.727, Kunming, 650500 Yunnan China
- />Biological Big Data College, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| |
Collapse
|
130
|
Sheshadri SA, Nishanth MJ, Simon B. Stress-Mediated cis-Element Transcription Factor Interactions Interconnecting Primary and Specialized Metabolism in planta. FRONTIERS IN PLANT SCIENCE 2016; 7:1725. [PMID: 27933071 PMCID: PMC5122738 DOI: 10.3389/fpls.2016.01725] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 11/02/2016] [Indexed: 05/07/2023]
Abstract
Plant specialized metabolites are being used worldwide as therapeutic agents against several diseases. Since the precursors for specialized metabolites come through primary metabolism, extensive investigations have been carried out to understand the detailed connection between primary and specialized metabolism at various levels. Stress regulates the expression of primary and specialized metabolism genes at the transcriptional level via transcription factors binding to specific cis-elements. The presence of varied cis-element signatures upstream to different stress-responsive genes and their transcription factor binding patterns provide a prospective molecular link among diverse metabolic pathways. The pattern of occurrence of these cis-elements (overrepresentation/common) decipher the mechanism of stress-responsive upregulation of downstream genes, simultaneously forming a molecular bridge between primary and specialized metabolisms. Though many studies have been conducted on the transcriptional regulation of stress-mediated primary or specialized metabolism genes, but not much data is available with regard to cis-element signatures and transcription factors that simultaneously modulate both pathway genes. Hence, our major focus would be to present a comprehensive analysis of the stress-mediated interconnection between primary and specialized metabolism genes via the interaction between different transcription factors and their corresponding cis-elements. In future, this study could be further utilized for the overexpression of the specific transcription factors that upregulate both primary and specialized metabolism, thereby simultaneously improving the yield and therapeutic content of plants.
Collapse
Affiliation(s)
| | | | - Bindu Simon
- School of Chemical and Biotechnology, SASTRA UniversityThanjavur, India
| |
Collapse
|
131
|
Evaluation of stability and validation of reference genes for RT-qPCR expression studies in rice plants under water deficit. J Appl Genet 2016; 58:163-177. [PMID: 27878453 DOI: 10.1007/s13353-016-0374-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 10/13/2016] [Accepted: 10/18/2016] [Indexed: 12/30/2022]
Abstract
Many studies use strategies that allow for the identification of a large number of genes expressed in response to different stress conditions to which the plant is subjected throughout its cycle. In order to obtain accurate and reliable results in gene expression studies, it is necessary to use reference genes, which must have uniform expression in the majority of cells in the organism studied. RNA isolation of leaves and expression analysis in real-time quantitative polymerase chain reaction (RT-qPCR) were carried out. In this study, nine candidate reference genes were tested, actin 11 (ACT11), ubiquitin conjugated to E2 enzyme (UBC-E2), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), beta tubulin (β-tubulin), eukaryotic initiation factor 4α (eIF-4α), ubiquitin 10 (UBQ10), ubiquitin 5 (UBQ5), aquaporin TIP41 (TIP41-Like) and cyclophilin, in two genotypes of rice, AN Cambará and BRS Querência, with different levels of soil moisture (20%, 10% and recovery) in the vegetative (V5) and reproductive stages (period preceding flowering). Currently, there are different softwares that perform stability analyses and define the most suitable reference genes for a particular study. In this study, we used five different methods: geNorm, BestKeeper, ΔCt method, NormFinder and RefFinder. The results indicate that UBC-E2 and UBQ5 can be used as reference genes in all samples and softwares evaluated. The genes β-tubulin and eIF-4α, traditionally used as reference genes, along with GAPDH, presented lower stability values. The gene expression of basic leucine zipper (bZIP23 and bZIP72) was used to validate the selected reference genes, demonstrating that the use of an inappropriate reference can induce erroneous results.
Collapse
|
132
|
Huang C, Zhou J, Jie Y, Xing H, Zhong Y, Yu W, She W, Ma Y, Liu Z, Zhang Y. A Ramie bZIP Transcription Factor BnbZIP2 Is Involved in Drought, Salt, and Heavy Metal Stress Response. DNA Cell Biol 2016; 35:776-786. [PMID: 27845851 DOI: 10.1089/dna.2016.3251] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
bZIP transcription factors play key roles in plant growth, development, and stress signaling. A bZIP gene BnbZIP2 (GenBank accession number: KP642148) was cloned from ramie. BnbZIP2 has a 1416 base pair open reading frame, encoding a 471 amino acid protein containing a characteristic bZIP domain and a leucine zipper. BnbZIP2 shares high sequence similarity with bZIP factors from other plants. The BnbZIP2 protein is localized to both nuclei and cytoplasm. Transcripts of BnbZIP2 were found in various tissues in ramie, with significantly higher levels in female and male flowers. Its expression was induced by drought, high salinity, and abscisic acid treatments. Analysis of the cis-elements in promoters of BnbZIP2 identified cis-acting elements involved in growth, developmental processes, and a variety of stress responses. Transgenic Arabidopsis plants' overexpression of BnbZIP2 exhibited more sensitivity to drought and heavy metal Cd stress during seed germination, whereas more tolerance to high-salinity stress than the wild type during both seed germination and plant development. Thus, BnbZIP2 may act as a positive regulator in plants' response to high-salinity stress and be an important candidate gene for molecular breeding of salt-tolerant plants.
Collapse
Affiliation(s)
- Chengjian Huang
- 1 Institute of Ramie, Hunan Agricultural University , Changsha, China .,2 Dazhou Institute of Agricultural Sciences , Dazhou, China
| | - Jinghua Zhou
- 1 Institute of Ramie, Hunan Agricultural University , Changsha, China .,3 College of Agronomy, Hunan Agricultural University , Changsha, China
| | - Yucheng Jie
- 1 Institute of Ramie, Hunan Agricultural University , Changsha, China .,3 College of Agronomy, Hunan Agricultural University , Changsha, China .,4 Hunan Provincial Crop Germplasm Innovation and Utilization Laboratory , Changsha, China
| | - Hucheng Xing
- 1 Institute of Ramie, Hunan Agricultural University , Changsha, China .,3 College of Agronomy, Hunan Agricultural University , Changsha, China .,4 Hunan Provincial Crop Germplasm Innovation and Utilization Laboratory , Changsha, China
| | - Yingli Zhong
- 4 Hunan Provincial Crop Germplasm Innovation and Utilization Laboratory , Changsha, China .,5 College of Bioscience and Biotechnology, Hunan Agricultural University , Changsha, China
| | - Weilin Yu
- 1 Institute of Ramie, Hunan Agricultural University , Changsha, China .,4 Hunan Provincial Crop Germplasm Innovation and Utilization Laboratory , Changsha, China
| | - Wei She
- 1 Institute of Ramie, Hunan Agricultural University , Changsha, China .,3 College of Agronomy, Hunan Agricultural University , Changsha, China
| | - Yushen Ma
- 1 Institute of Ramie, Hunan Agricultural University , Changsha, China .,3 College of Agronomy, Hunan Agricultural University , Changsha, China .,4 Hunan Provincial Crop Germplasm Innovation and Utilization Laboratory , Changsha, China
| | - Zehang Liu
- 1 Institute of Ramie, Hunan Agricultural University , Changsha, China .,3 College of Agronomy, Hunan Agricultural University , Changsha, China
| | - Ying Zhang
- 1 Institute of Ramie, Hunan Agricultural University , Changsha, China .,3 College of Agronomy, Hunan Agricultural University , Changsha, China .,4 Hunan Provincial Crop Germplasm Innovation and Utilization Laboratory , Changsha, China
| |
Collapse
|
133
|
Liu H, Dong S, Sun D, Liu W, Gu F, Liu Y, Guo T, Wang H, Wang J, Chen Z. CONSTANS-Like 9 (OsCOL9) Interacts with Receptor for Activated C-Kinase 1(OsRACK1) to Regulate Blast Resistance through Salicylic Acid and Ethylene Signaling Pathways. PLoS One 2016; 11:e0166249. [PMID: 27829023 PMCID: PMC5102437 DOI: 10.1371/journal.pone.0166249] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 10/25/2016] [Indexed: 11/19/2022] Open
Abstract
In a previous transcriptome analysis of early response genes in rice during Magnaporthe oryzae infection, we identified a CONSTANS-like (COL) gene OsCOL9. In the present study, we investigated the functional roles of OsCOL9 in blast resistance. OsCOL9 belonged to group II of the COL protein family, and it contained a BB-box and a C-terminal CCT (CONSTANS, COL and TOC1) domain. OsCOL9 was found in the nucleus of rice cells, and it exerted transcriptional activation activities through its middle region (MR). Magnaporthe oryzae infection induced OsCOL9 expression, and transgenic OsCOL9 knock-out rice plants showed increased pathogen susceptibility. OsCOL9 was a critical regulator of pathogen-related genes, especially PR1b, which were also activated by exogenous salicylic acid (SA) and 1-aminocyclopropane-1-carboxylicacid (ACC), the precursor of ethylene (ET). Further analysis indicated that OsCOL9 over-expression increased the expressions of phytohormone biosynthetic genes, NPR1, WRKY45, OsACO1 and OsACS1, which were related to SA and ET biosynthesis. Interestingly, we found that OsCOL9 physically interacted with the scaffold protein OsRACK1 through its CCT domain, and the OsRACK1 expression was induced in response to exogenous SA and ACC as well as M. oryzae infection. Taken together, these results indicated that the COL protein OsCOL9 interacted with OsRACK1, and it enhanced the rice blast resistance through SA and ET signaling pathways.
Collapse
Affiliation(s)
- Hao Liu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Shuangyu Dong
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Dayuan Sun
- Plant Protection Research Institute Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, 510640, China
| | - Wei Liu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Fengwei Gu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Yongzhu Liu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Hui Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Jiafeng Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
- * E-mail: (JW); (ZC)
| | - Zhiqiang Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
- * E-mail: (JW); (ZC)
| |
Collapse
|
134
|
Padder BA, Kamfwa K, Awale HE, Kelly JD. Transcriptome Profiling of the Phaseolus vulgaris - Colletotrichum lindemuthianum Pathosystem. PLoS One 2016; 11:e0165823. [PMID: 27829044 PMCID: PMC5102369 DOI: 10.1371/journal.pone.0165823] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/18/2016] [Indexed: 01/08/2023] Open
Abstract
Bean (Phaseolus vulgaris) anthracnose caused by the hemi-biotrophic pathogen Colletotrichum lindemuthianum is a major factor limiting production worldwide. Although sources of resistance have been identified and characterized, the early molecular events in the host-pathogen interface have not been investigated. In the current study, we conducted a comprehensive transcriptome analysis using Illumina sequencing of two near isogenic lines (NILs) differing for the presence of the Co-1 gene on chromosome Pv01 during a time course following infection with race 73 of C. lindemuthianum. From this, we identified 3,250 significantly differentially expressed genes (DEGs) within and between the NILs over the time course of infection. During the biotrophic phase the majority of DEGs were up regulated in the susceptible NIL, whereas more DEGs were up-regulated in the resistant NIL during the necrotrophic phase. Various defense related genes, such as those encoding PR proteins, peroxidases, lipoxygenases were up regulated in the resistant NIL. Conversely, genes encoding sugar transporters were up-regulated in the susceptible NIL during the later stages of infection. Additionally, numerous transcription factors (TFs) and candidate genes within the vicinity of the Co-1 locus were differentially expressed, suggesting a global reprogramming of gene expression in and around the Co-1 locus. Through this analysis, we reduced the previous number of candidate genes reported at the Co-1 locus from eight to three. These results suggest the dynamic nature of P. vulgaris-C. lindemuthianum interaction at the transcriptomic level and reflect the role of both pathogen and effector triggered immunity on changes in plant gene expression.
Collapse
Affiliation(s)
- Bilal A. Padder
- Dept. of Plant, Soil and Microbial Sciences, Michigan State Univ., 1066 Bogue St., East Lansing, MI, 48824, United States of America
| | - Kelvin Kamfwa
- Dept. of Plant, Soil and Microbial Sciences, Michigan State Univ., 1066 Bogue St., East Lansing, MI, 48824, United States of America
| | - Halima E. Awale
- Dept. of Plant, Soil and Microbial Sciences, Michigan State Univ., 1066 Bogue St., East Lansing, MI, 48824, United States of America
| | - James D. Kelly
- Dept. of Plant, Soil and Microbial Sciences, Michigan State Univ., 1066 Bogue St., East Lansing, MI, 48824, United States of America
| |
Collapse
|
135
|
Lozano-Sotomayor P, Chávez Montes RA, Silvestre-Vañó M, Herrera-Ubaldo H, Greco R, Pablo-Villa J, Galliani BM, Diaz-Ramirez D, Weemen M, Boutilier K, Pereira A, Colombo L, Madueño F, Marsch-Martínez N, de Folter S. Altered expression of the bZIP transcription factor DRINK ME affects growth and reproductive development in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:437-451. [PMID: 27402171 DOI: 10.1111/tpj.13264] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 06/24/2016] [Accepted: 07/06/2016] [Indexed: 05/05/2023]
Abstract
Here we describe an uncharacterized gene that negatively influences Arabidopsis growth and reproductive development. DRINK ME (DKM; bZIP30) is a member of the bZIP transcription factor family, and is expressed in meristematic tissues such as the inflorescence meristem (IM), floral meristem (FM), and carpel margin meristem (CMM). Altered DKM expression affects meristematic tissues and reproductive organ development, including the gynoecium, which is the female reproductive structure and is determinant for fertility and sexual reproduction. A microarray analysis indicates that DKM overexpression affects the expression of cell cycle, cell wall, organ initiation, cell elongation, hormone homeostasis, and meristem activity genes. Furthermore, DKM can interact in yeast and in planta with proteins involved in shoot apical meristem maintenance such as WUSCHEL, KNAT1/BP, KNAT2 and JAIBA, and with proteins involved in medial tissue development in the gynoecium such as HECATE, BELL1 and NGATHA1. Taken together, our results highlight the relevance of DKM as a negative modulator of Arabidopsis growth and reproductive development.
Collapse
Affiliation(s)
- Paulina Lozano-Sotomayor
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Gto., México
| | - Ricardo A Chávez Montes
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Gto., México
| | - Marina Silvestre-Vañó
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Campus de la Universidad Politécnica de Valencia, 46022, Valencia, Spain
| | - Humberto Herrera-Ubaldo
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Gto., México
| | | | - Jeanneth Pablo-Villa
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Gto., México
| | - Bianca M Galliani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - David Diaz-Ramirez
- Departamento de Biotecnología y Bioquímica, CINVESTAV-IPN, Irapuato, Gto., México
| | - Mieke Weemen
- Wageningen University and Research Centre, Bioscience, P.O. Box 619, 6700 AP, Wageningen, The Netherlands
| | - Kim Boutilier
- Wageningen University and Research Centre, Bioscience, P.O. Box 619, 6700 AP, Wageningen, The Netherlands
| | - Andy Pereira
- Crop, Soil and Environmental Sciences, University of Arkansas, 115 Plant Science Building, Fayetteville, AR, 72701, USA
| | - Lucia Colombo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Francisco Madueño
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Campus de la Universidad Politécnica de Valencia, 46022, Valencia, Spain
| | | | - Stefan de Folter
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Gto., México
| |
Collapse
|
136
|
Van Leene J, Blomme J, Kulkarni SR, Cannoot B, De Winne N, Eeckhout D, Persiau G, Van De Slijke E, Vercruysse L, Vanden Bossche R, Heyndrickx KS, Vanneste S, Goossens A, Gevaert K, Vandepoele K, Gonzalez N, Inzé D, De Jaeger G. Functional characterization of the Arabidopsis transcription factor bZIP29 reveals its role in leaf and root development. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:5825-5840. [PMID: 27660483 PMCID: PMC5066499 DOI: 10.1093/jxb/erw347] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plant bZIP group I transcription factors have been reported mainly for their role during vascular development and osmosensory responses. Interestingly, bZIP29 has been identified in a cell cycle interactome, indicating additional functions of bZIP29 in plant development. Here, bZIP29 was functionally characterized to study its role during plant development. It is not present in vascular tissue but is specifically expressed in proliferative tissues. Genome-wide mapping of bZIP29 target genes confirmed its role in stress and osmosensory responses, but also identified specific binding to several core cell cycle genes and to genes involved in cell wall organization. bZIP29 protein complex analyses validated interaction with other bZIP group I members and provided insight into regulatory mechanisms acting on bZIP dimers. In agreement with bZIP29 expression in proliferative tissues and with its binding to promoters of cell cycle regulators, dominant-negative repression of bZIP29 altered the cell number in leaves and in the root meristem. A transcriptome analysis on the root meristem, however, indicated that bZIP29 might regulate cell number through control of cell wall organization. Finally, ectopic dominant-negative repression of bZIP29 and redundant factors led to a seedling-lethal phenotype, pointing to essential roles for bZIP group I factors early in plant development.
Collapse
Affiliation(s)
- Jelle Van Leene
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Jonas Blomme
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Shubhada R Kulkarni
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Bernard Cannoot
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Nancy De Winne
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Dominique Eeckhout
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Geert Persiau
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Eveline Van De Slijke
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Leen Vercruysse
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Robin Vanden Bossche
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Ken S Heyndrickx
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Steffen Vanneste
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Alain Goossens
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, B-9000 Gent, Belgium Department of Biochemistry, Ghent University, B-9000 Gent, Belgium
| | - Klaas Vandepoele
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Nathalie Gonzalez
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, B-9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| |
Collapse
|
137
|
Yogendra KN, Kushalappa AC. Integrated transcriptomics and metabolomics reveal induction of hierarchies of resistance genes in potato against late blight. FUNCTIONAL PLANT BIOLOGY : FPB 2016; 43:766-782. [PMID: 32480502 DOI: 10.1071/fp16028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 04/15/2016] [Indexed: 05/11/2023]
Abstract
Late blight caused by Phytophthora infestans is a devastating disease affecting potato production worldwide. The quantitative resistance is durable, but the underlying molecular and biochemical mechanisms are poorly understood, limiting its application in breeding. Integrated transcriptomics and metabolomics approach was used for the first time to study the hierarchies of molecular events occurring, following inoculation of resistant and susceptible potato genotypes with P. infestans. RNA sequencing revealed a total of 4216 genes that were differentially expressed in the resistant than in the susceptible genotype. Genes that were highly expressed and associated with their biosynthetic metabolites that were highly accumulated, through metabolic pathway regulation, were selected. Quantitative real-time PCR was performed to confirm the RNA-seq expression levels. The induced leucine-rich repeat receptor-like kinases (LRR-RLKs) are considered to be involved in pathogen recognition. These receptor genes are considered to trigger downstream oxidative burst, phytohormone signalling-related genes, and transcription factors that regulated the resistance genes to produce resistance related metabolites to suppress the pathogen infection. It was noted that several resistance genes in metabolic pathways related to phenylpropanoids, flavonoids, alkaloids and terpenoid biosynthesis were strongly induced in the resistant genotypes. The pathway specific gene induction provided key insights into the metabolic reprogramming of induced defence responses in resistant genotypes.
Collapse
Affiliation(s)
| | - Ajjamada C Kushalappa
- Department of Plant Science, McGill University, Ste. Anne de Bellevue, Québec, Canada
| |
Collapse
|
138
|
Salih H, Leng X, He SP, Jia YH, Gong WF, Du XM. Characterization of the early fiber development gene, Ligon-lintless 1 (Li1), using microarray. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.plgene.2016.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
139
|
Tobias PA, Guest DI, Külheim C, Hsieh JF, Park RF. A curious case of resistance to a new encounter pathogen: myrtle rust in Australia. MOLECULAR PLANT PATHOLOGY 2016; 17:783-8. [PMID: 26575410 PMCID: PMC6638338 DOI: 10.1111/mpp.12331] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/07/2015] [Accepted: 10/07/2015] [Indexed: 05/28/2023]
Abstract
Resistance genes (R genes) in plants mediate a highly specific response to microbial pathogens, often culminating in localized cell death. Such resistance is generally pathogen race specific and believed to be the result of evolutionary selection pressure. Where a host and pathogen do not share an evolutionary history, specific resistance is expected to be absent or rare. Puccinia psidii, the causal agent of myrtle rust, was recently introduced to Australia, a continent rich in myrtaceous taxa. Responses within species to this new pathogen range from full susceptibility to resistance. Using the myrtle rust case study, we examine models to account for the presence of resistance to new encounter pathogens, such as the retention of ancient R genes through prolonged 'trench warfare', pairing of resistance gene products and the guarding of host integrity.
Collapse
Affiliation(s)
- Peri A Tobias
- Department of Plant and Food Sciences, Faculty of Agriculture and Environment, University of Sydney, Eveleigh, NSW, 2015, Australia
| | - David I Guest
- Department of Plant and Food Sciences, Faculty of Agriculture and Environment, University of Sydney, Eveleigh, NSW, 2015, Australia
| | - Carsten Külheim
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Ji-Fan Hsieh
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Robert F Park
- Department of Plant and Food Sciences, Faculty of Agriculture and Environment, University of Sydney, Plant Breeding Institute, Narellan, NSW, 2567, Australia
| |
Collapse
|
140
|
Shen L, Liu Z, Yang S, Yang T, Liang J, Wen J, Liu Y, Li J, Shi L, Tang Q, Shi W, Hu J, Liu C, Zhang Y, Lin W, Wang R, Yu H, Mou S, Hussain A, Cheng W, Cai H, He L, Guan D, Wu Y, He S. Pepper CabZIP63 acts as a positive regulator during Ralstonia solanacearum or high temperature-high humidity challenge in a positive feedback loop with CaWRKY40. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:2439-51. [PMID: 26936828 PMCID: PMC4809298 DOI: 10.1093/jxb/erw069] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
CaWRKY40 is known to act as a positive regulator in the response of pepper (Capsicum annuum) to Ralstonia solanacearum inoculation (RSI) or high temperature-high humidity (HTHH), but the underlying mechanism remains elusive. Herein, we report that CabZIP63, a pepper bZIP family member, participates in this process by regulating the expression of CaWRKY40. CabZIP63 was found to localize in the nuclei, be up-regulated by RSI or HTHH, bind to promoters of both CabZIP63(pCabZIP63) and CaWRKY40(pCaWRKY40), and activate pCabZIP63- and pCaWRKY40-driven β-glucuronidase expression in a C- or G-box-dependent manner. Silencing of CabZIP63 by virus-induced gene silencing (VIGS) in pepper plants significantly attenuated their resistance to RSI and tolerance to HTHH, accompanied by down-regulation of immunity- or thermotolerance-associated CaPR1, CaNPR1, CaDEF1, and CaHSP24. Hypersensitive response-mediated cell death and expression of the tested immunity- and thermotolerance-associated marker genes were induced by transient overexpression (TOE) of CabZIP63, but decreased by that of CabZIP63-SRDX. Additionally, binding of CabZIP63 to pCaWRKY40 was up-regulated by RSI or HTHH, and the transcript level of CaWRKY40 and binding of CaWRKY40 to the promoters of CaPR1, CaNPR1, CaDEF1 and CaHSP24 were up-regulated by TOE of CabZIP63. On the other hand, CabZIP63 was also up-regulated transcriptionally by TOE of CaWRKY40. The data suggest collectively that CabZIP63 directly or indirectly regulates the expression of CaWRKY40 at both the transcriptional and post-transcriptional level, forming a positive feedback loop with CaWRKY40 during pepper's response to RSI or HTHH. Altogether, our data will help to elucidate the underlying mechanism of crosstalk between pepper's response to RSI and HTHH.
Collapse
Affiliation(s)
- Lei Shen
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Zhiqin Liu
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Sheng Yang
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Tong Yang
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Jiaqi Liang
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Jiayu Wen
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Yanyan Liu
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Jiazhi Li
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Lanping Shi
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Qian Tang
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Wei Shi
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Jiong Hu
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Cailing Liu
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Yangwen Zhang
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Wei Lin
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Rongzhang Wang
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Huanxin Yu
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Shaoliang Mou
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Ansar Hussain
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Wei Cheng
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Hanyang Cai
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Li He
- College of Life Science, Jinggang Shan University, Ji'an, Jiangxi 343000, PR China
| | - Deyi Guan
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Yang Wu
- College of Life Science, Jinggang Shan University, Ji'an, Jiangxi 343000, PR China
| | - Shuilin He
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| |
Collapse
|
141
|
Shan W, Chen JY, Kuang JF, Lu WJ. Banana fruit NAC transcription factor MaNAC5 cooperates with MaWRKYs to enhance the expression of pathogenesis-related genes against Colletotrichum musae. MOLECULAR PLANT PATHOLOGY 2016; 17:330-8. [PMID: 26033522 PMCID: PMC6638545 DOI: 10.1111/mpp.12281] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Plants respond to pathogen attack by the modulation of a large set of genes, which are regulated by different types of transcription factor (TF). NAC (NAM/ATAF/CUC) and WRKY are plant-specific families of TFs, and have received much attention as transcriptional regulators in plant pathogen defence. However, the cooperation between NAC and WRKY TFs in the disease response remains largely unknown. Our previous study has revealed that two banana fruit WRKY TFs, MaWRKY1 and MaWRKY2, are involved in salicylic acid (SA)- and methyl jasmonate (MeJA)-induced resistance against Colletotrichum musae via binding to promoters of pathogenesis-related (PR) genes. Here, we found that MaNAC1, MaNAC2 and MaNAC5 were up-regulated after C. musae infection, and were also significantly enhanced by SA and MeJA treatment. Protein-protein interaction analysis showed that MaNAC5 physically interacted with MaWRKY1 and MaWRKY2. More importantly, dual-luciferase reporter (DLR) assay revealed that MaNAC5, MaWRKY1 and MaWRKY2 were transcriptional activators, and individually or cooperatively activated the transcriptional activities of MaPR1-1, MaPR2, MaPR10c and MaCHIL1 genes. Collectively, our results indicate that MaNAC5 cooperates with MaWRKY1 and MaWRKY2 to regulate the expression of a specific set of PR genes in the disease response, and to contribute at least partially to SA- and MeJA-induced pathogen resistance.
Collapse
Affiliation(s)
- Wei Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
| | - Jian-Ye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
| | - Jian-Fei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
| | - Wang-Jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Key Laboratory for Postharvest Science, College of Horticultural Science, South China Agricultural University, Guangzhou, 510642, China
| |
Collapse
|
142
|
In silico analysis of Mn transporters (NRAMP1) in various plant species. Mol Biol Rep 2016; 43:151-63. [PMID: 26878855 DOI: 10.1007/s11033-016-3950-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 02/09/2016] [Indexed: 01/18/2023]
Abstract
Manganese (Mn) is an essential micronutrient in plant life cycle. It may be involved in photosynthesis, carbohydrate and lipid biosynthesis, and oxidative stress protection. Mn deficiency inhibits the plant growth and development, and causes the various plant symptoms such as interveinal chlorosis and tissue necrosis. Despite its importance in plant life cycle, we still have limited knowledge about Mn transporters in many plant species. Therefore, this study aimed to identify and characterize high affinity Arabidopsis Mn root transporter NRAMP1 orthologs in 17 different plant species. Various in silico methods and digital gene expression data were used in identification and characterization of NRAMP1 homologs; physico-chemical properties of sequences were calculated, putative transmembrane domains (TMDs) and conserved motif signatures were determined, phylogenetic tree was constructed, 3D models and interactome map were generated, and gene expression data was analyzed. 49 NRAMP1 homologs were identified from proteome datasets of 17 plant species using AtNRAMP1 as query. Identified sequences were characterized with a NRAMP domain structure, 10-12 putative TMDs with cytosolic N- and C-terminuses, and 10-14 exons encoding a protein of 500-588 amino acids and 53.8-64.3 kDa molecular weight with basic characteristics. Consensus transport residues, GQSSTITGTYAGQY(/F)V(/I)MQGFLD(/E/N) between TMD-8 and 9 were identified in all sequences but putative N-linked glycosylation sites were not highly conserved. In phylogeny, NRAMP1 sequences demonstrated divergence in lower and higher plants as well as in monocots and dicots. Despite divergence of lower plant Physcomitrella patens in phylogeny, it showed similarity in superposed 3D models. Phylogenetic distribution of AtNRAMP1 and 6 homologs inferred a functional relationship to NRAMP6 sequences in Mn transport, while distribution of OsNRAMP1 and 5 homologs implicated an involvement of NRAMP1 sequences in Mn transport or a cross-talk between in Fe-Mn homeostasis. Interactome analysis further confirmed this cross-talk between Mn and Fe pathways. Gene expression profile of AtNRAMP1 under Fe-, K-, P- and S-deficiencies, and cold, drought, heat and salt stresses revealed various proteins involving in transcription regulation, cofactor biosynthesis, diverse developmental roles, carbohydrate metabolism, oxidation-reduction reactions, cellular signaling and protein degradation pathways. Mn deficiency or toxicity could cause serious adverse effects in plants as well as in humans. To reduce these adversities mainly rely on understanding the molecular mechanisms underlying Mn uptake from the soil. However, we still have limited knowledge regarding the structural and functional roles of Mn transporters in many plant species. Therefore, identification and characterization of Mn root uptake transporter, NRAMP1 orthologs in various plant species will provide valuable theoretical knowledge to better understand Mn transporters as well as it may become an insight for future studies aiming to develop genetically engineered and biofortified plants.
Collapse
|
143
|
Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation. Sci Rep 2016; 6:18936. [PMID: 26729541 PMCID: PMC4733048 DOI: 10.1038/srep18936] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 12/01/2015] [Indexed: 11/12/2022] Open
Abstract
Gene expression variation largely contributes to phenotypic diversity and constructing pan-transcriptome is considered necessary for species with complex genomes. However, the regulation mechanisms and functional consequences of pan-transcriptome is unexplored systematically. By analyzing RNA-seq data from 368 maize diverse inbred lines, we identified almost one-third nuclear genes under expression presence and absence variation, which tend to play regulatory roles and are likely regulated by distant eQTLs. The ePAV was directly used as “genotype” to perform GWAS for 15 agronomic phenotypes and 526 metabolic traits to efficiently explore the associations between transcriptomic and phenomic variations. Through a modified assembly strategy, 2,355 high-confidence novel sequences with total 1.9 Mb lengths were found absent within reference genome. Ten randomly selected novel sequences were fully validated with genomic PCR, including another two NBS_LRR candidates potentially affect flavonoids and disease-resistance. A simulation analysis suggested that the pan-transcriptome of the maize whole kernel is approaching a maximum value of 63,000 genes, and through developing two test-cross populations and surveying several most important yield traits, the dispensable genes were shown to contribute to heterosis. Novel perspectives and resources to discover maize quantitative trait variations were provided to better understand the kernel regulation networks and to enhance maize breeding.
Collapse
|
144
|
Ouyang Z, Liu S, Huang L, Hong Y, Li X, Huang L, Zhang Y, Zhang H, Li D, Song F. Tomato SlERF.A1, SlERF.B4, SlERF.C3 and SlERF.A3, Members of B3 Group of ERF Family, Are Required for Resistance to Botrytis cinerea. FRONTIERS IN PLANT SCIENCE 2016; 7:1964. [PMID: 28083004 PMCID: PMC5187353 DOI: 10.3389/fpls.2016.01964] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 12/12/2016] [Indexed: 05/11/2023]
Abstract
The Ethylene-Responsive Factors (ERFs) comprise a large family of transcriptional factors that play critical roles in plant immunity. Gray mold disease caused by Botrytis cinerea, a typical necrotrophic fungal pathogen, is the serious disease that threatens tomato production worldwide. However, littler is known about the molecular mechanism regulating the immunity to B. cinerea in tomato. In the present study, virus-induced gene silencing (VIGS)-based functional analyses of 18 members of B3 group (also called Group IX) in tomato ERF family were performed to identify putative ERFs that are involved in disease resistance against B. cinerea. VIGS-based silencing of either SlERF.B1 or SlERF.C2 had lethal effect while silencing of SlERF.A3 (Pit4) significantly suppressed vegetative growth of tomato plants. Importantly, silencing of SlERF.A1, SlERF.A3, SlERF.B4, or SlERF.C3 resulted in increased susceptibility to B. cinerea, attenuated the B. cinerea-induced expression of jasmonic acid/ethylene-mediated signaling responsive defense genes and promoted the B. cinerea-induced H2O2 accumulation. However, silencing of SlERF.A3 also decreased the resistance against Pseudomonas syringae pv. tomato (Pst) DC3000 but silencing of SlERF.A1, SlERF.B4 or SlERF.C3 did not affect the resistance to this bacterial pathogen. Expression of SlERF.A1, SlERF.A3, SlERF.B4, or SlERF.C3 was induced by B. cinerea and by defense signaling hormones such as salicylic acid, methyl jasmonate, and 1-aminocyclopropane-1-carboxylic acid (an ethylene precursor). SlERF.A1, SlERF.B4, SlERF.C3, and SlERF.A3 proteins were found to localize in nucleus of cells and possess transactivation activity in yeasts. These data suggest that SlERF.A1, SlERF.B4, and SlERF.C3, three previously uncharacterized ERFs in B3 group, and SlERF.A3, a previously identified ERF with function in immunity to Pst DC3000, play important roles in resistance against B. cinerea in tomato.
Collapse
Affiliation(s)
- Zhigang Ouyang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang UniversityHangzhou, China
- National Navel Orange Engineering Research Center, College of Life and Environmental Sciences, Gannan Normal UniversityGanzhou, China
| | - Shixia Liu
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang UniversityHangzhou, China
| | - Lihong Huang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang UniversityHangzhou, China
| | - Yongbo Hong
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang UniversityHangzhou, China
| | - Xiaohui Li
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang UniversityHangzhou, China
| | - Lei Huang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang UniversityHangzhou, China
| | - Yafen Zhang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang UniversityHangzhou, China
| | - Huijuan Zhang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang UniversityHangzhou, China
| | - Dayong Li
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang UniversityHangzhou, China
| | - Fengming Song
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang UniversityHangzhou, China
- *Correspondence: Fengming Song,
| |
Collapse
|
145
|
Zhang L, Long Y, Fu C, Xiang J, Gan J, Wu G, Jia H, Yu L, Li M. Different Gene Expression Patterns between Leaves and Flowers in Lonicera japonica Revealed by Transcriptome Analysis. FRONTIERS IN PLANT SCIENCE 2016; 7:637. [PMID: 27242839 PMCID: PMC4861853 DOI: 10.3389/fpls.2016.00637] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 04/25/2016] [Indexed: 05/20/2023]
Abstract
The perennial and evergreen twining vine, Lonicera japonica is an important herbal medicine with great economic value. However, gene expression information for flowers and leaves of L. japonica remains elusive, which greatly impedes functional genomics research on this species. In this study, transcriptome profiles from leaves and flowers of L. japonica were examined using next-generation sequencing technology. A total of 239.41 million clean reads were used for de novo assembly with Trinity software, which generated 150,523 unigenes with N50 containing 947 bp. All the unigenes were annotated using Nr, SwissProt, COGs (Clusters of Orthologous Groups), GO (Gene Ontology), and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases. A total of 35,327 differentially expressed genes (DEGs, P ≤ 0.05) between leaves and flowers were detected. Among them, a total of 6602 DEGs were assigned with important biological processes including "Metabolic process," "Response to stimulus," "Cellular process," and etc. KEGG analysis showed that three possible enzymes involved in the biosynthesis of chlorogenic acid were up-regulated in flowers. Furthermore, the TF-based regulation network in L. japonica identified three differentially expressed transcription factors between leaves and flowers, suggesting distinct regulatory roles in L. japonica. Taken together, this study has provided a global picture of differential gene expression patterns between leaves and flowers in L japonica, providing a useful genomic resource that can also be used for functional genomics research on L. japonica in the future.
Collapse
Affiliation(s)
- Libin Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Yan Long
- Institute of Biotechnology, Chinese Academy of Agricultural SciencesBeijing, China
| | - Chunhua Fu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Jun Xiang
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Jianping Gan
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Gang Wu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Haibo Jia
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Longjiang Yu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
- *Correspondence: Maoteng Li
| |
Collapse
|
146
|
Zhao J, Guo R, Guo C, Hou H, Wang X, Gao H. Evolutionary and Expression Analyses of the Apple Basic Leucine Zipper Transcription Factor Family. FRONTIERS IN PLANT SCIENCE 2016; 7:376. [PMID: 27066030 PMCID: PMC4811886 DOI: 10.3389/fpls.2016.00376] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 03/11/2016] [Indexed: 05/03/2023]
Abstract
Transcription factors (TFs) play essential roles in the regulatory networks controlling many developmental processes in plants. Members of the basic leucine (Leu) zipper (bZIP) TF family, which is unique to eukaryotes, are involved in regulating diverse processes, including flower and vascular development, seed maturation, stress signaling, and defense responses to pathogens. The bZIP proteins have a characteristic bZIP domain composed of a DNA-binding basic region and a Leu zipper dimerization region. In this study, we identified 112 apple (Malus domestica Borkh) bZIP TF-encoding genes, termed MdbZIP genes. Synteny analysis indicated that segmental and tandem duplication events, as well as whole genome duplication, have contributed to the expansion of the apple bZIP family. The family could be divided into 11 groups based on structural features of the encoded proteins, as well as on the phylogenetic relationship of the apple bZIP proteins to those of the model plant Arabidopsis thaliana (AtbZIP genes). Synteny analysis revealed that several paired MdbZIP genes and AtbZIP gene homologs were located in syntenic genomic regions. Furthermore, expression analyses of group A MdbZIP genes showed distinct expression levels in 10 different organs. Moreover, changes in these expression profiles in response to abiotic stress conditions and various hormone treatments identified MdbZIP genes that were responsive to high salinity and drought, as well as to different phytohormones.
Collapse
Affiliation(s)
- Jiao Zhao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F UniversityYangling, China
| | - Rongrong Guo
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, China
| | - Chunlei Guo
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F UniversityYangling, China
| | - Hongmin Hou
- College of Horticulture, Qingdao Agricultural UniversityQingdao, China
| | - Xiping Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F UniversityYangling, China
- *Correspondence: Xiping Wang
| | - Hua Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F UniversityYangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F UniversityYangling, China
- Hua Gao
| |
Collapse
|
147
|
Alves MS, Soares ZG, Vidigal PMP, Barros EG, Poddanosqui AMP, Aoyagi LN, Abdelnoor RV, Marcelino-Guimarães FC, Fietto LG. Differential expression of four soybean bZIP genes during Phakopsora pachyrhizi infection. Funct Integr Genomics 2015; 15:685-96. [PMID: 26013145 DOI: 10.1007/s10142-015-0445-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 05/07/2015] [Accepted: 05/18/2015] [Indexed: 11/26/2022]
Abstract
Asian soybean rust (ASR), caused by the obligate biotrophic fungus Phakopsora pachyrhizi, is one of most important diseases in the soybean (Glycine max (L.) Merr.) agribusiness. The identification and characterization of genes related to plant defense responses to fungal infection are essential to develop ASR-resistant plants. In this work, we describe four soybean genes, GmbZIP62, GmbZIP105, GmbZIPE1, and GmbZIPE2, which encode transcription factors containing a basic leucine zipper (bZIP) domain from two divergent classes, and that are responsive to P. pachyrhizi infection. Molecular phylogenetic analyses demonstrated that these genes encode proteins similar to bZIP factors responsive to pathogens. Yeast transactivation assays showed that only GmbZIP62 has strong transactivation activity in yeast. In addition, three of the bZIP transcription factors analyzed were also differentially expressed by plant defense hormones, and all were differentially expressed by fungal attack, indicating that these proteins might participate in response to ASR infection. The results suggested that these bZIP proteins are part of the plant defense response to P. pachyrhizi infection, by regulating the gene expression related to ASR infection responses. These bZIP genes are potential targets to obtain new soybean genotypes resistant to ASR.
Collapse
Affiliation(s)
- Murilo S Alves
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil
| | - Zamira G Soares
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil
| | - Pedro M P Vidigal
- Núcleo de Análise de Biomoléculas, NuBioMol, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil
| | - Everaldo G Barros
- Universidade Católica de Brasília, 70790-160, Brasília, Distrito Federal, Brazil
| | | | | | | | | | - Luciano G Fietto
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil.
| |
Collapse
|
148
|
Alves MS, Soares ZG, Vidigal PMP, Barros EG, Poddanosqui AMP, Aoyagi LN, Abdelnoor RV, Marcelino-Guimarães FC, Fietto LG. Differential expression of four soybean bZIP genes during Phakopsora pachyrhizi infection. Funct Integr Genomics 2015. [PMID: 26013145 DOI: 10.1007/s10142-015-0445-440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Asian soybean rust (ASR), caused by the obligate biotrophic fungus Phakopsora pachyrhizi, is one of most important diseases in the soybean (Glycine max (L.) Merr.) agribusiness. The identification and characterization of genes related to plant defense responses to fungal infection are essential to develop ASR-resistant plants. In this work, we describe four soybean genes, GmbZIP62, GmbZIP105, GmbZIPE1, and GmbZIPE2, which encode transcription factors containing a basic leucine zipper (bZIP) domain from two divergent classes, and that are responsive to P. pachyrhizi infection. Molecular phylogenetic analyses demonstrated that these genes encode proteins similar to bZIP factors responsive to pathogens. Yeast transactivation assays showed that only GmbZIP62 has strong transactivation activity in yeast. In addition, three of the bZIP transcription factors analyzed were also differentially expressed by plant defense hormones, and all were differentially expressed by fungal attack, indicating that these proteins might participate in response to ASR infection. The results suggested that these bZIP proteins are part of the plant defense response to P. pachyrhizi infection, by regulating the gene expression related to ASR infection responses. These bZIP genes are potential targets to obtain new soybean genotypes resistant to ASR.
Collapse
Affiliation(s)
- Murilo S Alves
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil
| | - Zamira G Soares
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil
| | - Pedro M P Vidigal
- Núcleo de Análise de Biomoléculas, NuBioMol, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil
| | - Everaldo G Barros
- Universidade Católica de Brasília, 70790-160, Brasília, Distrito Federal, Brazil
| | | | | | | | | | - Luciano G Fietto
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil.
| |
Collapse
|
149
|
Li D, Fu F, Zhang H, Song F. Genome-wide systematic characterization of the bZIP transcriptional factor family in tomato (Solanum lycopersicum L.). BMC Genomics 2015. [PMID: 26459863 DOI: 10.1186/s12864-015-1990-1996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND Transcription factors of the basic leucine zipper (bZIP) family represent exclusively in eukaryotes and have been shown to regulate diverse biological processes in plant growth and development as well as in abiotic and biotic stress responses. However, little is known about the bZIP family in tomato (Solanum lycopersicum L.). METHODS The SlbZIP genes were identified using local BLAST and hidden Markov model profile searches. The phylogenetic trees, conserved motifs and gene structures were generated by MEGA6.06, MEME tool and gene Structure Display Server, respectively. The syntenic block diagrams were generated by the Circos software. The transcriptional gene expression profiles were obtained using Genevestigator tool and quantitative RT-PCR. RESULTS In the present study, we carried out a genome-wide identification and systematic analyses of 69 SlbZIP genes that distributes unevenly on the tomato chromosomes. This family can be divided into 9 groups according to the phylogenetic relationship among the SlbZIP proteins. Six kinds of intron patterns (a-f) within the basic and hinge regions are defined. The additional conserved motifs and their presence of the group specificity were also identified. Further, we predicted the DNA-binding patterns and the dimerization property on the basis of the characteristic features in the basic and hinge regions and the leucine zipper, respectively, which supports our classification greatly and helps to classify 24 distinct subfamilies. Within the SlbZIP family, a total of 40 SlbZIP genes are located in the segmental duplicate regions in the tomato genome, suggesting that the segment chromosomal duplications contribute greatly to the expansion of the tomato SlbZIP family. Expression profiling analyses of 59 SlbZIP genes using quantitative RT-PCR and publicly available microarray data indicate that the tomato SlbZIP genes have distinct and diverse expression patterns in different tissues and developmental stages and many of the tomato bZIP genes might be involved in responses to various abiotic and biotic stresses as well as in response to light. CONCLUSIONS This genome-wide systematic characterization identified a total of 69 members in the SlbZIP family and the analyses of the protein features and gene expression patterns provide useful clues for further functional characterization of the bZIP transcription factors in tomato.
Collapse
Affiliation(s)
- Dayong Li
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Fuyou Fu
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN, 47907, USA
| | - Huijuan Zhang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Fengming Song
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| |
Collapse
|
150
|
Li D, Fu F, Zhang H, Song F. Genome-wide systematic characterization of the bZIP transcriptional factor family in tomato (Solanum lycopersicum L.). BMC Genomics 2015; 16:771. [PMID: 26459863 PMCID: PMC4603586 DOI: 10.1186/s12864-015-1990-6] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 10/06/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transcription factors of the basic leucine zipper (bZIP) family represent exclusively in eukaryotes and have been shown to regulate diverse biological processes in plant growth and development as well as in abiotic and biotic stress responses. However, little is known about the bZIP family in tomato (Solanum lycopersicum L.). METHODS The SlbZIP genes were identified using local BLAST and hidden Markov model profile searches. The phylogenetic trees, conserved motifs and gene structures were generated by MEGA6.06, MEME tool and gene Structure Display Server, respectively. The syntenic block diagrams were generated by the Circos software. The transcriptional gene expression profiles were obtained using Genevestigator tool and quantitative RT-PCR. RESULTS In the present study, we carried out a genome-wide identification and systematic analyses of 69 SlbZIP genes that distributes unevenly on the tomato chromosomes. This family can be divided into 9 groups according to the phylogenetic relationship among the SlbZIP proteins. Six kinds of intron patterns (a-f) within the basic and hinge regions are defined. The additional conserved motifs and their presence of the group specificity were also identified. Further, we predicted the DNA-binding patterns and the dimerization property on the basis of the characteristic features in the basic and hinge regions and the leucine zipper, respectively, which supports our classification greatly and helps to classify 24 distinct subfamilies. Within the SlbZIP family, a total of 40 SlbZIP genes are located in the segmental duplicate regions in the tomato genome, suggesting that the segment chromosomal duplications contribute greatly to the expansion of the tomato SlbZIP family. Expression profiling analyses of 59 SlbZIP genes using quantitative RT-PCR and publicly available microarray data indicate that the tomato SlbZIP genes have distinct and diverse expression patterns in different tissues and developmental stages and many of the tomato bZIP genes might be involved in responses to various abiotic and biotic stresses as well as in response to light. CONCLUSIONS This genome-wide systematic characterization identified a total of 69 members in the SlbZIP family and the analyses of the protein features and gene expression patterns provide useful clues for further functional characterization of the bZIP transcription factors in tomato.
Collapse
Affiliation(s)
- Dayong Li
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Fuyou Fu
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN, 47907, USA
| | - Huijuan Zhang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Fengming Song
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| |
Collapse
|