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Felemban A, Moreno JC, Mi J, Ali S, Sham A, AbuQamar SF, Al-Babili S. The apocarotenoid β-ionone regulates the transcriptome of Arabidopsis thaliana and increases its resistance against Botrytis cinerea. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:541-560. [PMID: 37932864 DOI: 10.1111/tpj.16510] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 11/08/2023]
Abstract
Carotenoids are isoprenoid pigments indispensable for photosynthesis. Moreover, they are the precursor of apocarotenoids, which include the phytohormones abscisic acid (ABA) and strigolactones (SLs) as well as retrograde signaling molecules and growth regulators, such as β-cyclocitral and zaxinone. Here, we show that the application of the volatile apocarotenoid β-ionone (β-I) to Arabidopsis plants at micromolar concentrations caused a global reprogramming of gene expression, affecting thousands of transcripts involved in stress tolerance, growth, hormone metabolism, pathogen defense, and photosynthesis. This transcriptional reprogramming changes, along with induced changes in the level of the phytohormones ABA, jasmonic acid, and salicylic acid, led to enhanced Arabidopsis resistance to the widespread necrotrophic fungus Botrytis cinerea (B.c.) that causes the gray mold disease in many crop species and spoilage of harvested fruits. Pre-treatment of tobacco and tomato plants with β-I followed by inoculation with B.c. confirmed the effect of β-I in increasing the resistance to this pathogen in crop plants. Moreover, we observed reduced susceptibility to B.c. in fruits of transgenic tomato plants overexpressing LYCOPENE β-CYCLASE, which contains elevated levels of endogenous β-I, providing a further evidence for its effect on B.c. infestation. Our work unraveled β-I as a further carotenoid-derived regulatory metabolite and indicates the possibility of establishing this natural volatile as an environmentally friendly bio-fungicide to control B.c.
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Affiliation(s)
- Abrar Felemban
- The Bioactives Laboratory, Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering Division, 4700 King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Juan C Moreno
- The Bioactives Laboratory, Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering Division, 4700 King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Jianing Mi
- The Bioactives Laboratory, Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering Division, 4700 King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Shawkat Ali
- Kentville Research and Development Center, Agriculture and Agri-Food Canada, Kentville, Nova Scotia, B4N 1J5, Canada
| | - Arjun Sham
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Synan F AbuQamar
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Salim Al-Babili
- The Bioactives Laboratory, Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering Division, 4700 King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
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Wang Y, Meng W, Ye Y, Yu X, Chen H, Liu Y, Xu M, Wang N, Qi F, Lan Y, Xu Y, Ma J, Zhang C. Transcriptome-Wide Analysis of Core Transcription Factors Associated with Defense Responses in Autotetraploid versus Diploid Rice under Saline Stress and Recovery. Int J Mol Sci 2023; 24:15982. [PMID: 37958969 PMCID: PMC10650042 DOI: 10.3390/ijms242115982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023] Open
Abstract
Saline stress is a major abiotic stress that inhibits plant growth and yields worldwide. The plant transcription factor (TF) family plays an important role in converting abiotic stress signals into gene expression changes. In this study, a transcriptome-based comparative analysis was performed to investigate the global gene expression of all the TFs in diploid and autotetraploid rice during the early stage of NaCl stress and recovery period. The phenotypic data indicated that the tetraploid rice exhibited a superior salt-tolerant ability compared to the diploid rice. A total of 55 TF families were co-expressed in the tetraploid and diploid rice, and the cumulative number of TF-expressed genes was relatively higher in the diploid rice than in the tetraploid rice at all time points. Unlike the diploid rice, the overall gene expression levels of the tetraploid rice were comparable to the control during recovery. The number of differentially expressed TFs (DE-TFs) in the tetraploid rice decreased after recovery, whereas it increased to a large extent in the diploid rice. GO and KEGG pathway enrichment analysis of the DE-TFs discovered the early switching of the ABA-activated signaling pathway and specific circadian rhythm in the tetraploid rice. Combining the PPI network and heatmap analysis, some core DE-TFs were found that may have potential roles to play in tetraploid salt tolerance. This study will pave the way for elucidating the complex network regulatory mechanisms of salt tolerance in tetraploid rice.
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Affiliation(s)
- Yingkai Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (Y.W.); (W.M.); (Y.Y.); (X.Y.); (H.C.); (Y.L.); (M.X.); (N.W.); (F.Q.); (Y.L.); (Y.X.)
| | - Weilong Meng
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (Y.W.); (W.M.); (Y.Y.); (X.Y.); (H.C.); (Y.L.); (M.X.); (N.W.); (F.Q.); (Y.L.); (Y.X.)
| | - Yan Ye
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (Y.W.); (W.M.); (Y.Y.); (X.Y.); (H.C.); (Y.L.); (M.X.); (N.W.); (F.Q.); (Y.L.); (Y.X.)
| | - Xinfang Yu
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (Y.W.); (W.M.); (Y.Y.); (X.Y.); (H.C.); (Y.L.); (M.X.); (N.W.); (F.Q.); (Y.L.); (Y.X.)
| | - Haiyuan Chen
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (Y.W.); (W.M.); (Y.Y.); (X.Y.); (H.C.); (Y.L.); (M.X.); (N.W.); (F.Q.); (Y.L.); (Y.X.)
| | - Yuchen Liu
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (Y.W.); (W.M.); (Y.Y.); (X.Y.); (H.C.); (Y.L.); (M.X.); (N.W.); (F.Q.); (Y.L.); (Y.X.)
| | - Minghong Xu
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (Y.W.); (W.M.); (Y.Y.); (X.Y.); (H.C.); (Y.L.); (M.X.); (N.W.); (F.Q.); (Y.L.); (Y.X.)
| | - Ningning Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (Y.W.); (W.M.); (Y.Y.); (X.Y.); (H.C.); (Y.L.); (M.X.); (N.W.); (F.Q.); (Y.L.); (Y.X.)
- Jilin Provincial Laboratory of Crop Germplasm Resources, Changchun 130000, China
| | - Fan Qi
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (Y.W.); (W.M.); (Y.Y.); (X.Y.); (H.C.); (Y.L.); (M.X.); (N.W.); (F.Q.); (Y.L.); (Y.X.)
| | - Yujie Lan
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (Y.W.); (W.M.); (Y.Y.); (X.Y.); (H.C.); (Y.L.); (M.X.); (N.W.); (F.Q.); (Y.L.); (Y.X.)
| | - Yan Xu
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (Y.W.); (W.M.); (Y.Y.); (X.Y.); (H.C.); (Y.L.); (M.X.); (N.W.); (F.Q.); (Y.L.); (Y.X.)
| | - Jian Ma
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (Y.W.); (W.M.); (Y.Y.); (X.Y.); (H.C.); (Y.L.); (M.X.); (N.W.); (F.Q.); (Y.L.); (Y.X.)
- Jilin Provincial Laboratory of Crop Germplasm Resources, Changchun 130000, China
| | - Chunying Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (Y.W.); (W.M.); (Y.Y.); (X.Y.); (H.C.); (Y.L.); (M.X.); (N.W.); (F.Q.); (Y.L.); (Y.X.)
- Jilin Provincial Laboratory of Crop Germplasm Resources, Changchun 130000, China
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Luo D, Sun W, Cai J, Hu G, Zhang D, Zhang X, Larkin RM, Zhang J, Yang C, Ye Z, Wang T. SlBBX20 attenuates JA signalling and regulates resistance to Botrytis cinerea by inhibiting SlMED25 in tomato. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:792-805. [PMID: 36582069 PMCID: PMC10037119 DOI: 10.1111/pbi.13997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/13/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
Jasmonic acid (JA) plays an important role in regulating plant growth and defence responses. Here, we show that a transcription factor that belongs to the B-box (BBX) family named SlBBX20 regulates resistance to Botrytis cinerea in tomato by modulating JA signalling. The response to JA was significantly suppressed when SlBBX20 was overexpressed in tomato. By contrast, the JA response was enhanced in SlBBX20 knockout lines. RNA sequencing analysis provided more evidence that SlBBX20 modulates the expression of genes that are involved in JA signalling. We found that SlBBX20 interacts with SlMED25, a subunit of the Mediator transcriptional co-activator complex, and prevents the accumulation of the SlMED25 protein and transcription of JA-responsive genes. JA contributes to the defence response against necrotrophic pathogens. Knocking out SlBBX20 or overexpressing SlMED25 enhanced tomato resistance to B. cinerea. The resistance was impaired when SlBBX20 was overexpressed in plants that also overexpressed SlMED25. These data show that SlBBX20 attenuates JA signalling by regulating SlMED25. Interestingly, in addition to developing enhanced resistance to B. cinerea, SlBBX20-KO plants also produced higher fruit yields. SlBBX20 is a potential target gene for efforts that aim to develop elite crop varieties using gene editing technologies.
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Affiliation(s)
- Dan Luo
- Key Laboratory of Horticulture Plant Biology, Ministry of EducationHuazhong Agriculture UniversityWuhanChina
| | - Wenhui Sun
- Key Laboratory of Horticulture Plant Biology, Ministry of EducationHuazhong Agriculture UniversityWuhanChina
| | - Jun Cai
- Key Laboratory of Horticulture Plant Biology, Ministry of EducationHuazhong Agriculture UniversityWuhanChina
| | - Guoyu Hu
- Key Laboratory of Horticulture Plant Biology, Ministry of EducationHuazhong Agriculture UniversityWuhanChina
| | - Danqiu Zhang
- Key Laboratory of Horticulture Plant Biology, Ministry of EducationHuazhong Agriculture UniversityWuhanChina
| | - Xiaoyan Zhang
- Key Laboratory of Horticulture Plant Biology, Ministry of EducationHuazhong Agriculture UniversityWuhanChina
| | - Robert M. Larkin
- Key Laboratory of Horticulture Plant Biology, Ministry of EducationHuazhong Agriculture UniversityWuhanChina
| | - Junhong Zhang
- Key Laboratory of Horticulture Plant Biology, Ministry of EducationHuazhong Agriculture UniversityWuhanChina
| | - Changxian Yang
- Key Laboratory of Horticulture Plant Biology, Ministry of EducationHuazhong Agriculture UniversityWuhanChina
| | - Zhibiao Ye
- Key Laboratory of Horticulture Plant Biology, Ministry of EducationHuazhong Agriculture UniversityWuhanChina
| | - Taotao Wang
- Key Laboratory of Horticulture Plant Biology, Ministry of EducationHuazhong Agriculture UniversityWuhanChina
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Decoding Metabolic Reprogramming in Plants under Pathogen Attacks, a Comprehensive Review of Emerging Metabolomics Technologies to Maximize Their Applications. Metabolites 2023; 13:metabo13030424. [PMID: 36984864 PMCID: PMC10055942 DOI: 10.3390/metabo13030424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/01/2023] [Accepted: 03/09/2023] [Indexed: 03/15/2023] Open
Abstract
In their environment, plants interact with a multitude of living organisms and have to cope with a large variety of aggressions of biotic or abiotic origin. What has been known for several decades is that the extraordinary variety of chemical compounds the plants are capable of synthesizing may be estimated in the range of hundreds of thousands, but only a fraction has been fully characterized to be implicated in defense responses. Despite the vast importance of these metabolites for plants and also for human health, our knowledge about their biosynthetic pathways and functions is still fragmentary. Recent progress has been made particularly for the phenylpropanoids and oxylipids metabolism, which is more emphasized in this review. With an increasing interest in monitoring plant metabolic reprogramming, the development of advanced analysis methods should now follow. This review capitalizes on the advanced technologies used in metabolome mapping in planta, including different metabolomics approaches, imaging, flux analysis, and interpretation using bioinformatics tools. Advantages and limitations with regards to the application of each technique towards monitoring which metabolite class or type are highlighted, with special emphasis on the necessary future developments to better mirror such intricate metabolic interactions in planta.
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Velásquez-Zapata V, Elmore JM, Fuerst G, Wise RP. An interolog-based barley interactome as an integration framework for immune signaling. Genetics 2022; 221:iyac056. [PMID: 35435213 PMCID: PMC9157089 DOI: 10.1093/genetics/iyac056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/04/2022] [Indexed: 12/12/2022] Open
Abstract
The barley MLA nucleotide-binding leucine-rich-repeat (NLR) receptor and its orthologs confer recognition specificity to many fungal diseases, including powdery mildew, stem-, and stripe rust. We used interolog inference to construct a barley protein interactome (Hordeum vulgare predicted interactome, HvInt) comprising 66,133 edges and 7,181 nodes, as a foundation to explore signaling networks associated with MLA. HvInt was compared with the experimentally validated Arabidopsis interactome of 11,253 proteins and 73,960 interactions, verifying that the 2 networks share scale-free properties, including a power-law distribution and small-world network. Then, by successive layering of defense-specific "omics" datasets, HvInt was customized to model cellular response to powdery mildew infection. Integration of HvInt with expression quantitative trait loci (eQTL) enabled us to infer disease modules and responses associated with fungal penetration and haustorial development. Next, using HvInt and infection-time-course RNA sequencing of immune signaling mutants, we assembled resistant and susceptible subnetworks. The resulting differentially coexpressed (resistant - susceptible) interactome is essential to barley immunity, facilitates the flow of signaling pathways and is linked to mildew resistance locus a (Mla) through trans eQTL associations. Lastly, we anchored HvInt with new and previously identified interactors of the MLA coiled coli + nucleotide-binding domains and extended these to additional MLA alleles, orthologs, and NLR outgroups to predict receptor localization and conservation of signaling response. These results link genomic, transcriptomic, and physical interactions during MLA-specified immunity.
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Affiliation(s)
- Valeria Velásquez-Zapata
- Program in Bioinformatics & Computational Biology, Iowa State University, Ames, IA 50011, USA
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA
| | - James Mitch Elmore
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA
- Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Ames, IA 50011, USA
| | - Gregory Fuerst
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA
- Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Ames, IA 50011, USA
| | - Roger P Wise
- Program in Bioinformatics & Computational Biology, Iowa State University, Ames, IA 50011, USA
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA
- Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Ames, IA 50011, USA
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Ojeda-Martinez D, Diaz I, Santamaria ME. Transcriptomic Landscape of Herbivore Oviposition in Arabidopsis: A Systematic Review. FRONTIERS IN PLANT SCIENCE 2022; 12:772492. [PMID: 35126411 PMCID: PMC8815302 DOI: 10.3389/fpls.2021.772492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Herbivore oviposition produces all sorts of responses in plants, involving wide and complex genetic rearrangements. Many transcriptomic studies have been performed to understand this interaction, producing a bulk of transcriptomic data. However, the use of many transcriptomic techniques across the years, the lack of comparable transcriptomic context at the time of publication, and the use of outdated databases are limitations to understand this biological process. The current analysis intends to retrieve oviposition studies and process them with up-to-date techniques and updated databases. To reduce heterogeneities, the same processing techniques were applied, and Arabidopsis was selected to avoid divergencies on plant taxa stress response strategies. By doing so, we intended to understand the major mechanisms and regulatory processes linked to oviposition response. Differentially expressed gene (DEG) identification and co-expression network-based analyses were the main tools to achieve this goal. Two microarray studies and three RNA-seq analyses passed the screening criteria. The collected data pertained to the lepidopteran Pieris brassicae and the mite Tetranychus urticae, and covered a timeline from 3 to 144 h. Among the 18, 221 DEGs found, 15, 406 were exclusive of P. brassicae (72 h) and 801 were exclusive for the rest of the experiments. Excluding P. brassicae (72 h), shared genes on the rest of the experiments were twice the unique genes, indicating common response mechanisms were predominant. Enrichment analyses indicated that shared processes were circumscribed to earlier time points, and after 24 h, the divergences escalated. The response was characterized by patterns of time-dependent waves of unique processes. P. brassicae oviposition induced a rich response that shared functions across time points, while T. urticae eggs triggered less but more diverse time-dependent functions. The main processes altered were associated with hormonal cascades [e.g., salicilic acid (SA) and jasmonic acid (JA)], defense [reactive oxygen species (ROS) and glucosinolates], cell wall rearrangements, abiotic stress responses, and energy metabolism. Key gene drivers of the identified processes were also identified and presented. The current results enrich and clarify the information regarding the molecular behavior of the plant in response to oviposition by herbivores. This information is valuable for multiple stress response engineering tools, among other applications.
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Affiliation(s)
- Dairon Ojeda-Martinez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid – Instituto Nacional de Investigación y Tecnología Agraria y Alimentación, Madrid, Spain
| | - Isabel Diaz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid – Instituto Nacional de Investigación y Tecnología Agraria y Alimentación, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - M. Estrella Santamaria
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid – Instituto Nacional de Investigación y Tecnología Agraria y Alimentación, Madrid, Spain
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Quaglia M, Troni E, D’Amato R, Ederli L. Effect of zinc imbalance and salicylic acid co-supply on Arabidopsis response to fungal pathogens with different lifestyles. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:30-40. [PMID: 34608720 PMCID: PMC9291626 DOI: 10.1111/plb.13344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
In higher plants, Zn nutritional imbalance can affect growth, physiology and response to stress, with effect variable depending on host-pathogen interaction. Mechanisms through which Zn operates are not yet well known. The hormone salicylic acid (SA) can affect plant ion uptake, transport and defence responses. Thus, in this study the impact of Zn imbalance and SA co-supply on severity of infection with the necrotrophic fungal pathogen B. cinerea or the biotroph G. cichoracearum was assessed in A. thaliana Col-0. Spectrophotometric assays for pigments and malondialdehyde (MDA) content as a marker of lipid peroxidation, plant defensin 1.2 gene expression by semi-quantitative PCR, callose visualization by fluorescence microscopy and diseases evaluation by macro- and microscopic observations were carried out. Zinc plant concentration varied with the supplied dose. In comparison with the control, Zn-deficit or Zn-excess led to reduced chlorophyll content and PDF 1.2 transcripts induction. In Zn-deficient plants, where MDA increased, also the susceptibility to B. cinerea increased, whereas MDA decreased in G. cichoracearum. Zinc excess increased susceptibility to both pathogens. Co-administration of SA positively affected MDA level, callose deposition, PDF 1.2 transcripts and plant response to the two pathogens. The increased susceptibility to B. cinerea in both Zn-deficient and Zn-excess plants could be related to lack of induction of PDF 1.2 transcripts; oxidative stress could explain higher susceptibility to the necrotroph and lower susceptibility to the biotroph in Zn-deficient plants. This research shows that an appropriate evaluation of Zn supply according to the prevalent stress factor is desirable for plants.
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Affiliation(s)
- M. Quaglia
- Department of Agricultural, Food and Environmental SciencesUniversity of PerugiaPerugiaItaly
| | - E. Troni
- Department of Agricultural, Food and Environmental SciencesUniversity of PerugiaPerugiaItaly
| | - R. D’Amato
- Department of Agricultural, Food and Environmental SciencesUniversity of PerugiaPerugiaItaly
| | - L. Ederli
- Department of Agricultural, Food and Environmental SciencesUniversity of PerugiaPerugiaItaly
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8
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Vondras AM, Lerno L, Massonnet M, Minio A, Rowhani A, Liang D, Garcia J, Quiroz D, Figueroa‐Balderas R, Golino DA, Ebeler SE, Al Rwahnih M, Cantu D. Rootstock influences the effect of grapevine leafroll-associated viruses on berry development and metabolism via abscisic acid signalling. MOLECULAR PLANT PATHOLOGY 2021; 22:984-1005. [PMID: 34075700 PMCID: PMC8295520 DOI: 10.1111/mpp.13077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/17/2021] [Accepted: 04/19/2021] [Indexed: 05/14/2023]
Abstract
Grapevine leafroll-associated virus (GLRaV) infections are accompanied by symptoms influenced by host genotype, rootstock, environment, and which individual or combination of GLRaVs is present. Using a dedicated experimental vineyard, we studied the responses to GLRaVs in ripening berries from Cabernet Franc grapevines grafted to different rootstocks and with zero, one, or pairs of leafroll infection(s). RNA sequencing data were mapped to a high-quality Cabernet Franc genome reference assembled to carry out this study and integrated with hormone and metabolite abundance data. This study characterized conserved and condition-dependent responses to GLRaV infection(s). Common responses to GLRaVs were reproduced in two consecutive years and occurred in plants grafted to different rootstocks in more than one infection condition. Though different infections were inconsistently distinguishable from one another, the effects of infections in plants grafted to different rootstocks were distinct at each developmental stage. Conserved responses included the modulation of genes related to pathogen detection, abscisic acid (ABA) signalling, phenylpropanoid biosynthesis, and cytoskeleton remodelling. ABA, ABA glucose ester, ABA and hormone signalling-related gene expression, and the expression of genes in several transcription factor families differentiated the effects of GLRaVs in berries from Cabernet Franc grapevines grafted to different rootstocks. These results support that ABA participates in the shared responses to GLRaV infection and differentiates the responses observed in grapevines grafted to different rootstocks.
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Affiliation(s)
- Amanda M. Vondras
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Larry Lerno
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Mélanie Massonnet
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Andrea Minio
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Adib Rowhani
- Department of Plant PathologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Dingren Liang
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Jadran Garcia
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Daniela Quiroz
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCaliforniaUSA
| | | | - Deborah A. Golino
- Department of Plant PathologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Susan E. Ebeler
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Maher Al Rwahnih
- Department of Plant PathologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Dario Cantu
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCaliforniaUSA
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9
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Ederli L, Salerno G, Quaglia M. In the tripartite combination Botrytis cinerea-Arabidopsis-Eurydema oleracea, the fungal pathogen alters the plant-insect interaction via jasmonic acid signalling activation and inducible plant-emitted volatiles. JOURNAL OF PLANT RESEARCH 2021; 134:523-533. [PMID: 33738682 PMCID: PMC8106584 DOI: 10.1007/s10265-021-01273-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 02/19/2021] [Indexed: 05/28/2023]
Abstract
In ecosystems, plants are continuously challenged by combined stress conditions more than by a single biotic or abiotic factor. Consequently, in recent years studies on plant relationships with multiple stresses have aroused increasing interest. Here, the impact of inoculation with fungal pathogens with different lifestyles on Arabidopsis plants response to the following infestation with the invasive crop pest Eurydema oleracea was investigated. In particular, as fungal pathogens the necrotroph Botrytis cinerea and the biotroph Golovinomyces orontii were used. Plants exposed to B. cinerea, but not to G. orontii, showed reduced herbivore feeding damage. This difference was associated to different hormonal pathways triggered by the pathogens: G. orontii only induced the salicylate-mediated pathway, while B. cinerea stimulated also the jasmonate-dependent signalling, which persisted for a long time providing a long-term defence to further herbivore attack. In particular, the lower susceptibility of B. cinerea-infected Arabidopsis plants to E. oleracea was related to the stimulation of the JA-induced pathway on the production of plant volatile compounds, since treatment with VOCs emitted by B. cinerea inoculated plants inhibited both insect plant choice and feeding damage. These results indicate that necrotrophic plant pathogenic fungi modulate host volatile emission, thus affecting plant response to subsequent insect, thereby increasing the knowledge on tripartite plant-microbe-insect interactions in nature.
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Affiliation(s)
- Luisa Ederli
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, Perugia, 06121, Italy
| | - Gianandrea Salerno
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, Perugia, 06121, Italy.
| | - Mara Quaglia
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, Perugia, 06121, Italy
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10
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Shivhare D, Musialak-Lange M, Julca I, Gluza P, Mutwil M. Removing auto-activators from yeast-two-hybrid assays by conditional negative selection. Sci Rep 2021; 11:5477. [PMID: 33750818 PMCID: PMC7943551 DOI: 10.1038/s41598-021-84608-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 01/19/2021] [Indexed: 11/17/2022] Open
Abstract
Yeast-two-hybrid (Y2H) is widely used as a strategy to detect protein–protein interactions (PPIs). Recent advancements have made it possible to generate and analyse genome-wide PPI networks en masse by coupling Y2H with next-generation sequencing technology. However, one of the major challenges of yeast two-hybrid assay is the large amount of false-positive hits caused by auto-activators (AAs), which are proteins that activate the reporter genes without the presence of an interacting protein partner. Here, we have developed a negative selection to minimize these auto-activators by integrating the pGAL2-URA3 fragment into the yeast genome. Upon activation of the pGAL2 promoter by an AA, yeast cells expressing URA3 cannot grow in media supplemented with 5-Fluoroorotic acid (5-FOA). Hence, we selectively inhibit the growth of yeast cells expressing auto-activators and thus minimizing the amount of false-positive hits. Here, we have demonstrated that auto-activators can be successfully removed from a Marchantia polymorpha cDNA library using pGAL2-URA3 and 5-FOA treatment, in liquid and solid-grown cultures. Furthermore, since URA3 can also serve as a marker for uracil autotrophy, we propose that our approach is a valuable addition to any large-scale Y2H screen.
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Affiliation(s)
- Devendra Shivhare
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | | | - Irene Julca
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Pawel Gluza
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany.,School of Biosciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore. .,Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany.
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11
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Innate Resistance and Phosphite Treatment Affect Both the Pathogen's and Host's Transcriptomes in the Tanoak- Phytophthora ramorum Pathosystem. J Fungi (Basel) 2021; 7:jof7030198. [PMID: 33803362 PMCID: PMC7999100 DOI: 10.3390/jof7030198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/04/2021] [Accepted: 03/06/2021] [Indexed: 02/06/2023] Open
Abstract
Phosphites have been used to control Sudden Oak Death; however, their precise mode of action is not fully understood. To study the mechanism of action of phosphites, we conducted an inoculation experiment on two open-pollinated tanoak families, previously found to be partially resistant. Stems of treatment group individuals were sprayed with phosphite, and seven days later, distal leaves were inoculated with the Sudden Oak Death pathogen Phytophthora ramorum. Leaves from treated and untreated control plants were harvested before and seven days after inoculation, and transcriptomes of both host and pathogen were analyzed. We found that tanoak families differed in the presence of innate resistance (resistance displayed by untreated tanoak) and in the response to phosphite treatment. A set of expressed genes associated with innate resistance was found to overlap with an expressed gene set for phosphite-induced resistance. This observation may indicate that phosphite treatment increases the resistance of susceptible host plants. In addition, genes of the pathogen involved in detoxification were upregulated in phosphite-treated plants compared to phosphite-untreated plants. In summary, our RNA-Seq analysis supports a two-fold mode of action of phosphites, including a direct toxic effect on P. ramorum and an indirect enhancement of resistance in the tanoak host.
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12
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Sun J, Shi Q, Chen X, Liu R. Decoding the similarities and specific differences between latent and active tuberculosis infections based on consistently differential expression networks. Brief Bioinform 2019; 21:2084-2098. [PMID: 31724702 DOI: 10.1093/bib/bbz127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 08/21/2019] [Accepted: 09/06/2019] [Indexed: 11/14/2022] Open
Abstract
Although intensive efforts have been devoted to investigating latent tuberculosis (LTB) and active tuberculosis (PTB) infections, the similarities and differences in the host responses to these two closely associated stages remain elusive, probably due to the difficulty in identifying informative genes related to LTB using traditional methods. Herein, we developed a framework known as the consistently differential expression network to identify tuberculosis (TB)-related gene pairs by combining microarray profiles and protein-protein interactions. We thus obtained 774 and 693 pairs corresponding to the PTB and LTB stages, respectively. The PTB-specific genes showed higher expression values and fold-changes than the LTB-specific genes. Furthermore, the PTB-related pairs generally had higher expression correlations and would be more activated compared to their LTB-related counterparts. The module analysis implied that the detected gene pairs tended to cluster in the topological and functional modules. Functional analysis indicated that the LTB- and PTB-specific genes were enriched in different pathways and had remarkably different locations in the NF-κB signaling pathway. Finally, we showed that the identified genes and gene pairs had the potential to distinguish TB patients in different disease stages and could be considered as drug targets for the specific treatment of patients with LTB or PTB.
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Affiliation(s)
- Jun Sun
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Qianqian Shi
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xi Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Rong Liu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
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13
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Sukumari Nath V, Kumar Mishra A, Kumar A, Matoušek J, Jakše J. Revisiting the Role of Transcription Factors in Coordinating the Defense Response Against Citrus Bark Cracking Viroid Infection in Commercial Hop ( Humulus Lupulus L.). Viruses 2019; 11:v11050419. [PMID: 31060295 PMCID: PMC6563305 DOI: 10.3390/v11050419] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/29/2019] [Accepted: 05/03/2019] [Indexed: 01/13/2023] Open
Abstract
Transcription factors (TFs) play a major role in controlling gene expression by intricately regulating diverse biological processes such as growth and development, the response to external stimuli and the activation of defense responses. The systematic identification and classification of TF genes are essential to gain insight into their evolutionary history, biological roles, and regulatory networks. In this study, we performed a global mining and characterization of hop TFs and their involvement in Citrus bark cracking viroid CBCVd infection by employing a digital gene expression analysis. Our systematic analysis resulted in the identification of a total of 3,818 putative hop TFs that were classified into 99 families based on their conserved domains. A phylogenetic analysis classified the hop TFs into several subgroups based on a phylogenetic comparison with reference TF proteins from Arabidopsis thaliana providing glimpses of their evolutionary history. Members of the same subfamily and subgroup shared conserved motif compositions. The putative functions of the CBCVd-responsive hop TFs were predicted using their orthologous counterparts in A. thaliana. The analysis of the expression profiling of the CBCVd-responsive hop TFs revealed a massive differential modulation, and the expression of the selected TFs was validated using qRT-PCR. Together, the comprehensive integrated analysis in this study provides better insights into the TF regulatory networks associated with CBCVd infections in the hop, and also offers candidate TF genes for improving the resistance in hop against viroids.
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Affiliation(s)
- Vishnu Sukumari Nath
- Department of Molecular Genetics, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic.
| | - Ajay Kumar Mishra
- Department of Molecular Genetics, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic.
| | - Atul Kumar
- Department of Molecular Genetics, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic.
| | - Jaroslav Matoušek
- Department of Molecular Genetics, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic.
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia.
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14
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Jiang N, Cui J, Yang G, He X, Meng J, Luan Y. Comparative transcriptome analysis shows the defense response networks regulated by miR482b. PLANT CELL REPORTS 2019; 38:1-13. [PMID: 30191311 DOI: 10.1007/s00299-018-2344-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 09/02/2018] [Indexed: 06/08/2023]
Abstract
The transcriptomic profile in the leaves of miR482b-overexpressing tomato plants revealed that miR482b may suppress alpha-linolenic acid metabolism, cysteine and methionine metabolism, plant-pathogen interaction, and the MAPK pathway to reduce resistance to Phytophthora infestans. Our previous study showed that tomato miR482b acted as a negative regulator during tomato resistance to Phytophthora infestans by silencing NBS-LRR genes. To investigate pathways related to miR482b, the transcriptomic profile of tomato plants that overexpressed miR482b was constructed. A total of 47,124,670 raw sequence reads from the leaves of miR482b-overexpressing tomato plants were generated by Illumina sequencing. A total of 746 genes in miR482b-overexpressing tomato plants were found to show significantly differential expression relative to those in wild-type tomato plants, including 132 up-regulated genes and 614 down-regulated genes. GO and KEGG enrichment analyses showed that plant-pathogen interaction, the MAPK pathway, and the pathways related to JA and ET biosynthesis were affected by miR482b in tomato. qRT-PCR results showed that all the enriched genes in these pathways were down-regulated in tomato plants that overexpressed miR482b and up-regulated in tomato plants that overexpressed an NBS-LRR gene (Soly02g036270.2, the target gene of miR482b). After P. infestans infection, the expression of the enriched genes showed a time-dependent response, and the genes played different roles between resistant tomato (Solanum pimpinellifolium L3708) and tomato susceptible to P. infestans (S. lycopersicum Zaofen No. 2). Our results have, therefore, demonstrated that miR482b is an important component of defense response network. This will also help to identify candidate genes involved in plant-pathogen interaction.
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Affiliation(s)
- Ning Jiang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Jun Cui
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Guanglei Yang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Xiaoli He
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yushi Luan
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China.
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15
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Ramšak Ž, Coll A, Stare T, Tzfadia O, Baebler Š, Van de Peer Y, Gruden K. Network Modeling Unravels Mechanisms of Crosstalk between Ethylene and Salicylate Signaling in Potato. PLANT PHYSIOLOGY 2018; 178:488-499. [PMID: 29934298 PMCID: PMC6130022 DOI: 10.1104/pp.18.00450] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 06/09/2018] [Indexed: 05/25/2023]
Abstract
To develop novel crop breeding strategies, it is crucial to understand the mechanisms underlying the interaction between plants and their pathogens. Network modeling represents a powerful tool that can unravel properties of complex biological systems. In this study, we aimed to use network modeling to better understand immune signaling in potato (Solanum tuberosum). For this, we first built on a reliable Arabidopsis (Arabidopsis thaliana) immune signaling model, extending it with the information from diverse publicly available resources. Next, we translated the resulting prior knowledge network (20,012 nodes and 70,091 connections) to potato and superimposed it with an ensemble network inferred from time-resolved transcriptomics data for potato. We used different network modeling approaches to generate specific hypotheses of potato immune signaling mechanisms. An interesting finding was the identification of a string of molecular events illuminating the ethylene pathway modulation of the salicylic acid pathway through Nonexpressor of PR Genes1 gene expression. Functional validations confirmed this modulation, thus supporting the potential of our integrative network modeling approach for unraveling molecular mechanisms in complex systems. In addition, this approach can ultimately result in improved breeding strategies for potato and other sensitive crops.
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Affiliation(s)
- Živa Ramšak
- National Institute of Biology, Department of Biotechnology and Systems Biology, 1000 Ljubljana, Slovenia
| | - Anna Coll
- National Institute of Biology, Department of Biotechnology and Systems Biology, 1000 Ljubljana, Slovenia
| | - Tjaša Stare
- National Institute of Biology, Department of Biotechnology and Systems Biology, 1000 Ljubljana, Slovenia
| | - Oren Tzfadia
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Špela Baebler
- National Institute of Biology, Department of Biotechnology and Systems Biology, 1000 Ljubljana, Slovenia
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Kristina Gruden
- National Institute of Biology, Department of Biotechnology and Systems Biology, 1000 Ljubljana, Slovenia
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16
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Qi H, Jiang Z, Zhang K, Yang S, He F, Zhang Z. PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System. GENOMICS, PROTEOMICS & BIOINFORMATICS 2018; 16:283-293. [PMID: 30266409 PMCID: PMC6205082 DOI: 10.1016/j.gpb.2018.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 07/02/2018] [Accepted: 08/13/2018] [Indexed: 01/01/2023]
Abstract
High-throughput transcriptomics technologies have been widely used to study plant transcriptional reprogramming during the process of plant defense responses, and a large quantity of gene expression data have been accumulated in public repositories. However, utilization of these data is often hampered by the lack of standard metadata annotation. In this study, we curated 2444 public pathogenesis-related gene expression samples from the model plant Arabidopsis and three major crops (maize, rice, and wheat). We organized the data into a user-friendly database termed as PlaD. Currently, PlaD contains three key features. First, it provides large-scale curated data related to plant defense responses, including gene expression and gene functional annotation data. Second, it provides the visualization of condition-specific expression profiles. Third, it allows users to search co-regulated genes under the infections of various pathogens. Using PlaD, we conducted a large-scale transcriptome analysis to explore the global landscape of gene expression in the curated data. We found that only a small fraction of genes were differentially expressed under multiple conditions, which might be explained by their tendency of having more network connections and shorter network distances in gene networks. Collectively, we hope that PlaD can serve as an important and comprehensive knowledgebase to the community of plant sciences, providing insightful clues to better understand the molecular mechanisms underlying plant immune responses. PlaD is freely available at http://systbio.cau.edu.cn/plad/index.php or http://zzdlab.com/plad/index.php.
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Affiliation(s)
- Huan Qi
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhenhong Jiang
- Jiangxi Key Laboratory of Molecular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Kang Zhang
- Department of Plant Pathology and the Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Shiping Yang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Fei He
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China; Biology Department, Brookhaven National Lab, Upton, NY 11967, USA.
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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17
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Di Silvestre D, Bergamaschi A, Bellini E, Mauri P. Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World. Proteomes 2018; 6:proteomes6020027. [PMID: 29865292 PMCID: PMC6027444 DOI: 10.3390/proteomes6020027] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/30/2018] [Accepted: 06/01/2018] [Indexed: 12/26/2022] Open
Abstract
The investigation of plant organisms by means of data-derived systems biology approaches based on network modeling is mainly characterized by genomic data, while the potential of proteomics is largely unexplored. This delay is mainly caused by the paucity of plant genomic/proteomic sequences and annotations which are fundamental to perform mass-spectrometry (MS) data interpretation. However, Next Generation Sequencing (NGS) techniques are contributing to filling this gap and an increasing number of studies are focusing on plant proteome profiling and protein-protein interactions (PPIs) identification. Interesting results were obtained by evaluating the topology of PPI networks in the context of organ-associated biological processes as well as plant-pathogen relationships. These examples foreshadow well the benefits that these approaches may provide to plant research. Thus, in addition to providing an overview of the main-omic technologies recently used on plant organisms, we will focus on studies that rely on concepts of module, hub and shortest path, and how they can contribute to the plant discovery processes. In this scenario, we will also consider gene co-expression networks, and some examples of integration with metabolomic data and genome-wide association studies (GWAS) to select candidate genes will be mentioned.
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Affiliation(s)
- Dario Di Silvestre
- Institute for Biomedical Technologies-National Research Council; F.lli Cervi 93, 20090 Segrate, Milan, Italy.
| | - Andrea Bergamaschi
- Institute for Biomedical Technologies-National Research Council; F.lli Cervi 93, 20090 Segrate, Milan, Italy.
| | - Edoardo Bellini
- Institute for Biomedical Technologies-National Research Council; F.lli Cervi 93, 20090 Segrate, Milan, Italy.
| | - PierLuigi Mauri
- Institute for Biomedical Technologies-National Research Council; F.lli Cervi 93, 20090 Segrate, Milan, Italy.
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18
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Huang LY, Lin CW, Lee RH, Chiang CY, Wang YC, Chang CH, Huang HJ. Integrating Early Transcriptomic Responses to Rhizotoxins in Rice ( Oryza sativa. L.) Reveals Key Regulators and a Potential Early Biomarker of Cadmium Toxicity. FRONTIERS IN PLANT SCIENCE 2017; 8:1432. [PMID: 28868059 PMCID: PMC5563368 DOI: 10.3389/fpls.2017.01432] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 08/03/2017] [Indexed: 06/07/2023]
Abstract
As sessile organisms, plants were constantly challenged with biotic and abiotic stresses. Transcriptional activation of stress-responsive genes is a crucial part of the plant adaptation to environmental changes. Here, early response of rice root to eight rhizotoxic stressors: arsenate, copper, cadmium, mercury, chromate, vanadate, ferulic acid and juglone, was analyzed using published microarray data. There were 539 general stress response (GSR) genes up-regulated under all eight treatments, including genes related to carbohydrate metabolism, phytohormone balance, and cell wall structure. Genes related to transcriptional coactivation showed higher Ka/Ks ratio compared to the other GSR genes. Network analysis discovered complicated interaction within GSR genes and the most connected signaling hubs were WRKY53, WRKY71, and MAPK5. Promoter analysis discovers enriched SCGCGCS cis-element in GSR genes. Moreover, GSR genes tend to be intronless and genes with shorter total intron length were induced in a higher level. Among genes uniquely up-regulated by a single stress, a phosphoenolpyruvate carboxylase kinase (PPCK) was identified as a candidate biomarker for detecting cadmium contamination. Our findings provide insights into the transcriptome dynamics of molecular response of rice to different rhizotoxic stress and also demonstrate potential use of comparative transcriptome analysis in identifying a novel potential early biomarker.
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Affiliation(s)
- Li-Yao Huang
- Department of Life Sciences, National Cheng Kung UniversityTainan, Taiwan
| | - Chung-Wen Lin
- Department of Life Sciences, National Cheng Kung UniversityTainan, Taiwan
| | - Ruey-Hua Lee
- Institute of Tropical Plant Sciences, National Cheng Kung UniversityTainan, Taiwan
| | - Chih-Yun Chiang
- Department of Life Sciences, National Cheng Kung UniversityTainan, Taiwan
| | - Yung-Chuan Wang
- Department of Life Sciences, National Cheng Kung UniversityTainan, Taiwan
| | - Ching-Han Chang
- Department of Life Sciences, National Cheng Kung UniversityTainan, Taiwan
| | - Hao-Jen Huang
- Department of Life Sciences, National Cheng Kung UniversityTainan, Taiwan
- Institute of Tropical Plant Sciences, National Cheng Kung UniversityTainan, Taiwan
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19
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Mishra B, Sun Y, Ahmed H, Liu X, Mukhtar MS. Global temporal dynamic landscape of pathogen-mediated subversion of Arabidopsis innate immunity. Sci Rep 2017; 7:7849. [PMID: 28798368 PMCID: PMC5552879 DOI: 10.1038/s41598-017-08073-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/29/2017] [Indexed: 12/22/2022] Open
Abstract
The universal nature of networks’ structural and physical properties across diverse systems offers a better prospect to elucidate the interplay between a system and its environment. In the last decade, several large-scale transcriptome and interactome studies were conducted to understand the complex and dynamic nature of interactions between Arabidopsis and its bacterial pathogen, Pseudomonas syringae pv. tomato DC3000. We took advantage of these publicly available datasets and performed “-omics”-based integrative, and network topology analyses to decipher the transcriptional and protein-protein interaction activities of effector targets. We demonstrated that effector targets exhibit shorter distance to differentially expressed genes (DEGs) and possess increased information centrality. Intriguingly, effector targets are differentially expressed in a sequential manner and make for 1% of the total DEGs at any time point of infection with virulent or defense-inducing DC3000 strains. We revealed that DC3000 significantly alters the expression levels of 71% effector targets and their downstream physical interacting proteins in Arabidopsis interactome. Our integrative “-omics”-–based analyses identified dynamic complexes associated with MTI and disease susceptibility. Finally, we discovered five novel plant defense players using a systems biology-fueled top-to-bottom approach and demonstrated immune-related functions for them, further validating the power and resolution of our network analyses.
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Affiliation(s)
- Bharat Mishra
- Department of Biology, University of Alabama at Birmingham, Birmingham, USA
| | - Yali Sun
- Department of Biology, University of Alabama at Birmingham, Birmingham, USA
| | - Hadia Ahmed
- Department of Computer & Information Sciences, University of Alabama at Birmingham, Birmingham, USA
| | - Xiaoyu Liu
- Department of Biology, University of Alabama at Birmingham, Birmingham, USA
| | - M Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, Birmingham, USA. .,Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, USA.
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20
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Shigenaga AM, Berens ML, Tsuda K, Argueso CT. Towards engineering of hormonal crosstalk in plant immunity. CURRENT OPINION IN PLANT BIOLOGY 2017. [PMID: 28624670 DOI: 10.1016/j.pbi.2017.04.021] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Plant hormones regulate physiological responses in plants, including responses to pathogens and beneficial microbes. The last decades have provided a vast amount of evidence about the contribution of different plant hormones to plant immunity, and also of how they cooperate to orchestrate immunity activation, in a process known as hormone crosstalk. In this review we highlight the complexity of hormonal crosstalk in immunity and approaches currently being used to further understand this process, as well as perspectives to engineer hormone crosstalk for enhanced pathogen resistance and overall plant fitness.
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Affiliation(s)
- Alexandra M Shigenaga
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | - Matthias L Berens
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Kenichi Tsuda
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
| | - Cristiana T Argueso
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA.
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21
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Trigg SA, Garza RM, MacWilliams A, Nery JR, Bartlett A, Castanon R, Goubil A, Feeney J, O’Malley R, Huang SSC, Zhang ZZ, Galli M, Ecker JR. CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping. Nat Methods 2017; 14:819-825. [PMID: 28650476 PMCID: PMC5564216 DOI: 10.1038/nmeth.4343] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 05/16/2017] [Indexed: 01/25/2023]
Abstract
Broad-scale protein-protein interaction mapping is a major challenge given the cost, time, and sensitivity constraints of existing technologies. Here, we present a massively multiplexed yeast two-hybrid method, CrY2H-seq, which uses a Cre recombinase interaction reporter to intracellularly fuse the coding sequences of two interacting proteins and next-generation DNA sequencing to identify these interactions en masse. We applied CrY2H-seq to investigate sparsely annotated Arabidopsis thaliana transcription factors interactions. By performing ten independent screens testing a total of 36 million binary interaction combinations, and uncovering a network of 8,577 interactions among 1,453 transcription factors, we demonstrate CrY2H-seq's improved screening capacity, efficiency, and sensitivity over those of existing technologies. The deep-coverage network resource we call AtTFIN-1 recapitulates one-third of previously reported interactions derived from diverse methods, expands the number of known plant transcription factor interactions by three-fold, and reveals previously unknown family-specific interaction module associations with plant reproductive development, root architecture, and circadian coordination.
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Affiliation(s)
- Shelly A. Trigg
- Genomic Analysis and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA,Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Renee M. Garza
- Genomic Analysis and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Andrew MacWilliams
- Genomic Analysis and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Joseph R. Nery
- Genomic Analysis and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Anna Bartlett
- Genomic Analysis and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Rosa Castanon
- Genomic Analysis and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Adeline Goubil
- Genomic Analysis and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Joseph Feeney
- Genomic Analysis and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Ronan O’Malley
- Genomic Analysis and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Shao-shan Carol Huang
- Genomic Analysis and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Zhuzhu Z. Zhang
- Genomic Analysis and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Mary Galli
- Genomic Analysis and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Joseph R. Ecker
- Genomic Analysis and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA,Division of Biological Sciences, University of California San Diego, La Jolla, California, USA,Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California, USA,Correspondence should be addressed to J.R.E. ()
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22
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Jiang Z, He F, Zhang Z. Large-scale transcriptome analysis reveals arabidopsis metabolic pathways are frequently influenced by different pathogens. PLANT MOLECULAR BIOLOGY 2017; 94:453-467. [PMID: 28540497 DOI: 10.1007/s11103-017-0617-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 05/03/2017] [Indexed: 05/26/2023]
Abstract
Through large-scale transcriptional data analyses, we highlighted the importance of plant metabolism in plant immunity and identified 26 metabolic pathways that were frequently influenced by the infection of 14 different pathogens. Reprogramming of plant metabolism is a common phenomenon in plant defense responses. Currently, a large number of transcriptional profiles of infected tissues in Arabidopsis (Arabidopsis thaliana) have been deposited in public databases, which provides a great opportunity to understand the expression patterns of metabolic pathways during plant defense responses at the systems level. Here, we performed a large-scale transcriptome analysis based on 135 previously published expression samples, including 14 different pathogens, to explore the expression pattern of Arabidopsis metabolic pathways. Overall, metabolic genes are significantly changed in expression during plant defense responses. Upregulated metabolic genes are enriched on defense responses, and downregulated genes are enriched on photosynthesis, fatty acid and lipid metabolic processes. Gene set enrichment analysis (GSEA) identifies 26 frequently differentially expressed metabolic pathways (FreDE_Paths) that are differentially expressed in more than 60% of infected samples. These pathways are involved in the generation of energy, fatty acid and lipid metabolism as well as secondary metabolite biosynthesis. Clustering analysis based on the expression levels of these 26 metabolic pathways clearly distinguishes infected and control samples, further suggesting the importance of these metabolic pathways in plant defense responses. By comparing with FreDE_Paths from abiotic stresses, we find that the expression patterns of 26 FreDE_Paths from biotic stresses are more consistent across different infected samples. By investigating the expression correlation between transcriptional factors (TFs) and FreDE_Paths, we identify several notable relationships. Collectively, the current study will deepen our understanding of plant metabolism in plant immunity and provide new insights into disease-resistant crop improvement.
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Affiliation(s)
- Zhenhong Jiang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Fei He
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China.
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23
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Kim MS, Hong S, Devaraj SP, Im S, Kim JR, Lim YP. Identification and characterization of the leaf specific networks of inner and rosette leaves in Brassica rapa. Biochem Biophys Res Commun 2017. [PMID: 28647368 DOI: 10.1016/j.bbrc.2017.06.123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Inner and rosette leaves of Chinese cabbage (Brassica rapa) have different characteristics in terms of nutritional value, appearance, taste, color and texture. Many researchers have utilized differentially expressed genes for exploring the difference between inner and rosette leaves of Brassica rapa. The functional characteristics of a gene, however, is determined by complex interactions between genes. Hence, a noble network approach is required for elucidating such functional difference that is not captured by gene expression profiles alone. In this study, we measured gene expression in the standard cabbage genome by RNA-Sequencing and constructed rosette and inner leaf networks based on the gene expression profiles. Furthermore, we compared the topological and functional characteristics of these networks. We found significant functional difference between the rosette and inner leaf networks. Specifically, we found that the genes in the rosette leaf network were associated with homeostasis and response to external stimuli whereas the genes in the inner leaf network were mainly related to the glutamine biosynthesis processes and developmental processes with hormones. Overall, the network approach provides an insight into the functional difference of the two leaves.
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Affiliation(s)
- Man-Sun Kim
- Department of Horticulture, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, South Korea.
| | - Seongmin Hong
- Department of Horticulture, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, South Korea.
| | - Sangeeth Prasath Devaraj
- Department of Horticulture, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, South Korea.
| | - Subin Im
- Department of Horticulture, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, South Korea.
| | - Jeong-Rae Kim
- Department of Mathematics, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul 02504, South Korea.
| | - Yong Pyo Lim
- Department of Horticulture, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, South Korea.
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24
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Lin CW, Huang LY, Huang CL, Wang YC, Lai PH, Wang HV, Chang WC, Chiang TY, Huang HJ. Common Stress Transcriptome Analysis Reveals Functional and Genomic Architecture Differences Between Early and Delayed Response Genes. PLANT & CELL PHYSIOLOGY 2017; 58:546-559. [PMID: 28115496 DOI: 10.1093/pcp/pcx002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 01/02/2017] [Indexed: 06/06/2023]
Abstract
To identify the similarities among responses to diverse environmental stresses, we analyzed the transcriptome response of rice roots to three rhizotoxic perturbations (chromium, ferulic acid and mercury) and identified common early-transient, early-constant and delayed gene inductions. Common early response genes were mostly associated with signal transduction and hormones, and delayed response genes with lipid metabolism. Network component analysis revealed complicated interactions among common genes, the most highly connected signaling hubs being PP2C68, MPK5, LRR-RLK and NPR1. Gene architecture studies revealed different conserved promoter motifs and a different ratio of CpG island distribution between early and delayed genes. In addition, early-transient genes had more exons and a shorter first exon. IMEter was used to calculate the transcription regulation effects of introns, with greater effects for the first introns of early-transient than delayed genes. The higher Ka/Ks (non-synonymous/synonymous mutation) ratio of early-constant genes than early-transient, delayed and the genome median demonstrates the rapid evolution of early-constant genes. Our results suggest that finely tuned transcriptional control in response to environmental stress in rice depends on genomic architecture and signal intensity and duration.
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Affiliation(s)
- Chung-Wen Lin
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Li-Yao Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Chao-Li Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Yong-Chuan Wang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Pei-Hsuan Lai
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Hao-Ven Wang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Chi Chang
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Tzen-Yuh Chiang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Hao-Jen Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan
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25
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AbuQamar S, Moustafa K, Tran LS. Mechanisms and strategies of plant defense against Botrytis cinerea. Crit Rev Biotechnol 2017; 37:262-274. [PMID: 28056558 DOI: 10.1080/07388551.2016.1271767] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Biotic factors affect plant immune responses and plant resistance to pathogen infections. Despite the considerable progress made over the past two decades in manipulating genes, proteins and their levels from diverse sources, no complete genetic tolerance to environmental stresses has been developed so far in any crops. Plant defense response to pathogens, including Botrytis cinerea, is a complex biological process involving various changes at the biochemical, molecular (i.e. transcriptional) and physiological levels. Once a pathogen is detected, effective plant resistance activates signaling networks through the generation of small signaling molecules and the balance of hormonal signaling pathways to initiate defense mechanisms to the particular pathogen. Recently, studies using Arabidopsis thaliana and crop plants have shown that many genes are involved in plant responses to B. cinerea infection. In this article, we will review our current understanding of mechanisms regulating plant responses to B. cinerea with a particular interest on hormonal regulatory networks involving phytohormones salicylic acid (SA), jasmonic acid (JA), ethylene (ET) and abscisic acid (ABA). We will also highlight some potential gene targets that are promising for improving crop resistance to B. cinerea through genetic engineering and breeding programs. Finally, the role of biological control as a complementary and alternative disease management will be overviewed.
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Affiliation(s)
- Synan AbuQamar
- a Department of Biology , United Arab Emirates University , Al-Ain , UAE
| | - Khaled Moustafa
- b Conservatoire National des Arts et Métiers , Paris , France
| | - Lam Son Tran
- c Plant Abiotic Stress Research Group & Faculty of Applied Sciences , Ton Duc Thang University , Ho Chi Minh City , Vietnam.,d Signaling Pathway Research Unit , RIKEN Center for Sustainable Resource Science , Yokohama , Kanagawa , Japan
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26
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Differential Coexpression Analysis Reveals Extensive Rewiring of Arabidopsis Gene Coexpression in Response to Pseudomonas syringae Infection. Sci Rep 2016; 6:35064. [PMID: 27721457 PMCID: PMC5056366 DOI: 10.1038/srep35064] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 09/23/2016] [Indexed: 01/21/2023] Open
Abstract
Plant defense responses to pathogens involve massive transcriptional reprogramming. Recently, differential coexpression analysis has been developed to study the rewiring of gene networks through microarray data, which is becoming an important complement to traditional differential expression analysis. Using time-series microarray data of Arabidopsis thaliana infected with Pseudomonas syringae, we analyzed Arabidopsis defense responses to P. syringae through differential coexpression analysis. Overall, we found that differential coexpression was a common phenomenon of plant immunity. Genes that were frequently involved in differential coexpression tend to be related to plant immune responses. Importantly, many of those genes have similar average expression levels between normal plant growth and pathogen infection but have different coexpression partners. By integrating the Arabidopsis regulatory network into our analysis, we identified several transcription factors that may be regulators of differential coexpression during plant immune responses. We also observed extensive differential coexpression between genes within the same metabolic pathways. Several metabolic pathways, such as photosynthesis light reactions, exhibited significant changes in expression correlation between normal growth and pathogen infection. Taken together, differential coexpression analysis provides a new strategy for analyzing transcriptional data related to plant defense responses and new insights into the understanding of plant-pathogen interactions.
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AbuQamar SF, Moustafa K, Tran LSP. 'Omics' and Plant Responses to Botrytis cinerea. FRONTIERS IN PLANT SCIENCE 2016; 7:1658. [PMID: 27895649 PMCID: PMC5108755 DOI: 10.3389/fpls.2016.01658] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 10/20/2016] [Indexed: 05/20/2023]
Abstract
Botrytis cinerea is a dangerous plant pathogenic fungus with wide host ranges. This aggressive pathogen uses multiple weapons to invade and cause serious damages on its host plants. The continuing efforts of how to solve the "puzzle" of the multigenic nature of B. cinerea's pathogenesis and plant defense mechanisms against the disease caused by this mold, the integration of omic approaches, including genomics, transcriptomics, proteomics and metabolomics, along with functional analysis could be a potential solution. Omic studies will provide a foundation for development of genetic manipulation and breeding programs that will eventually lead to crop improvement and protection. In this mini-review, we will highlight the current progresses in research in plant stress responses to B. cinerea using high-throughput omic technologies. We also discuss the opportunities that omic technologies can provide to research on B. cinerea-plant interactions as an example showing the impacts of omics on agricultural research.
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Affiliation(s)
- Synan F. AbuQamar
- Department of Biology, United Arab Emirates UniversityAl Ain, UAE
- *Correspondence: Synan F. AbuQamar, Lam-Son P. Tran, ;
| | | | - Lam-Son P. Tran
- Plant Abiotic Stress Research Group & Faculty of Applied Sciences, Ton Duc Thang UniversityHo Chi Minh City, Vietnam
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- *Correspondence: Synan F. AbuQamar, Lam-Son P. Tran, ;
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Kuhn H, Kwaaitaal M, Kusch S, Acevedo-Garcia J, Wu H, Panstruga R. Biotrophy at Its Best: Novel Findings and Unsolved Mysteries of the Arabidopsis-Powdery Mildew Pathosystem. THE ARABIDOPSIS BOOK 2016; 14:e0184. [PMID: 27489521 PMCID: PMC4957506 DOI: 10.1199/tab.0184] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
It is generally accepted in plant-microbe interactions research that disease is the exception rather than a common outcome of pathogen attack. However, in nature, plants with symptoms that signify colonization by obligate biotrophic powdery mildew fungi are omnipresent. The pervasiveness of the disease and the fact that many economically important plants are prone to infection by powdery mildew fungi drives research on this interaction. The competence of powdery mildew fungi to establish and maintain true biotrophic relationships renders the interaction a paramount example of a pathogenic plant-microbe biotrophy. However, molecular details underlying the interaction are in many respects still a mystery. Since its introduction in 1990, the Arabidopsis-powdery mildew pathosystem has become a popular model to study molecular processes governing powdery mildew infection. Due to the many advantages that the host Arabidopsis offers in terms of molecular and genetic tools this pathosystem has great capacity to answer some of the questions of how biotrophic pathogens overcome plant defense and establish a persistent interaction that nourishes the invader while in parallel maintaining viability of the plant host.
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Affiliation(s)
- Hannah Kuhn
- RWTH Aachen University, Institute for Biology I, Unit of Plant
Molecular Cell Biology, Worringerweg 1, D-52056 Aachen, Germany
- Address correspondence to
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