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Zhao K, Ebrahimie E, Mohammadi-Dehcheshmeh M, Lewsey MG, Zheng L, Hoogenraad NJ. Transcriptomic signature of cancer cachexia by integration of machine learning, literature mining and meta-analysis. Comput Biol Med 2024; 172:108233. [PMID: 38452471 DOI: 10.1016/j.compbiomed.2024.108233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 01/23/2024] [Accepted: 02/25/2024] [Indexed: 03/09/2024]
Abstract
BACKGROUND Cancer cachexia is a severe metabolic syndrome marked by skeletal muscle atrophy. A successful clinical intervention for cancer cachexia is currently lacking. The study of cachexia mechanisms is largely based on preclinical animal models and the availability of high-throughput transcriptomic datasets of cachectic mouse muscles is increasing through the extensive use of next generation sequencing technologies. METHODS Cachectic mouse muscle transcriptomic datasets of ten different studies were combined and mined by seven attribute weighting models, which analysed both categorical variables and numerical variables. The transcriptomic signature of cancer cachexia was identified by attribute weighting algorithms and was used to evaluate the performance of eleven pattern discovery models. The signature was employed to find the best combination of drugs (drug repurposing) for developing cancer cachexia treatment strategies, as well as to evaluate currently used cachexia drugs by literature mining. RESULTS Attribute weighting algorithms ranked 26 genes as the transcriptomic signature of muscle from mice with cancer cachexia. Deep Learning and Random Forest models performed better in differentiating cancer cachexia cases based on muscle transcriptomic data. Literature mining revealed that a combination of melatonin and infliximab has negative interactions with 2 key genes (Rorc and Fbxo32) upregulated in the transcriptomic signature of cancer cachexia in muscle. CONCLUSIONS The integration of machine learning, meta-analysis and literature mining was found to be an efficient approach to identifying a robust transcriptomic signature for cancer cachexia, with implications for improving clinical diagnosis and management of this condition.
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Affiliation(s)
- Kening Zhao
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China; La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
| | - Esmaeil Ebrahimie
- Genomics Research Platform, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC, 3086, Australia; School of Animal and Veterinary Science, The University of Adelaide, Adelaide, SA 5371, Australia; School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Manijeh Mohammadi-Dehcheshmeh
- Genomics Research Platform, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC, 3086, Australia; School of Animal and Veterinary Science, The University of Adelaide, Adelaide, SA 5371, Australia.
| | - Mathew G Lewsey
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia; La Trobe Institute for Sustainable Agriculture and Food, Department of Plant, Animal and Soil Sciences, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia; Australian Research Council Centre of Excellence in Plants for Space, AgriBio Building, La Trobe University, Bundoora, VIC, 3086, Australia.
| | - Lei Zheng
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Nick J Hoogenraad
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia; Tumour Targeting Laboratory, Olivia Newton-John Cancer Research Institute, School of Cancer Medicine, La Trobe University, Melbourne, VIC, 3084, Australia.
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Nadiminti PP, Wilson SM, van de Meene A, Hao A, Humphries J, Ratcliffe J, Yi C, Peirats-Llobet M, Lewsey MG, Whelan J, Bacic A, Doblin MS. Spatiotemporal deposition of cell wall polysaccharides in oat endosperm during grain development. Plant Physiol 2023; 194:168-189. [PMID: 37862163 PMCID: PMC10756759 DOI: 10.1093/plphys/kiad566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 08/11/2023] [Accepted: 09/24/2023] [Indexed: 10/22/2023]
Abstract
Oat (Avena sativa) is a cereal crop whose grains are rich in (1,3;1,4)-β-D-glucan (mixed-linkage glucan or MLG), a soluble dietary fiber. In our study, we analyzed oat endosperm development in 2 Canadian varieties with differing MLG content and nutritional value. We confirmed that oat undergoes a nuclear type of endosperm development but with a shorter cellularization phase than barley (Hordeum vulgare). Callose and cellulose were the first polysaccharides to be detected in the early anticlinal cell walls at 11 days postemergence (DPE) of the panicle. Other polysaccharides such as heteromannan and homogalacturonan were deposited early in cellularization around 12 DPE after the first periclinal walls are laid down. In contrast to barley, heteroxylan deposition coincided with completion of cellularization and was detected from 14 DPE but was only detectable after demasking. Notably, MLG was the last polysaccharide to be laid down at 18 DPE within the differentiation phase, rather than during cellularization. In addition, differences in the spatiotemporal patterning of MLG were also observed between the 2 varieties. The lower MLG-containing cultivar AC Morgan (3.5% w/w groats) was marked by the presence of a discontinuous pattern of MLG labeling, while labeling in the same walls in CDC Morrison (5.6% w/w groats) was mostly even and continuous. RNA-sequencing analysis revealed higher transcript levels of multiple MLG biosynthetic cellulose synthase-like F (CSLF) and CSLH genes during grain development in CDC Morrison compared with AC Morgan that likely contributes to the increased abundance of MLG at maturity in CDC Morrison. CDC Morrison was also observed to have smaller endosperm cells with thicker walls than AC Morgan from cellularization onwards, suggesting the processes controlling cell size and shape are established early in development. This study has highlighted that the molecular processes influencing MLG content and deposition are more complex than previously imagined.
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Affiliation(s)
- Pavani P Nadiminti
- La Trobe Institute for Sustainable Agriculture & Food, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Sarah M Wilson
- La Trobe Institute for Sustainable Agriculture & Food, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Allison van de Meene
- School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Alfie Hao
- La Trobe Institute for Sustainable Agriculture & Food, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria 3086, Australia
| | - John Humphries
- La Trobe Institute for Sustainable Agriculture & Food, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Julian Ratcliffe
- Latrobe University Bioimaging Platform, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Changyu Yi
- La Trobe Institute for Sustainable Agriculture & Food, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Marta Peirats-Llobet
- La Trobe Institute for Sustainable Agriculture & Food, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Mathew G Lewsey
- La Trobe Institute for Sustainable Agriculture & Food, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria 3086, Australia
| | - James Whelan
- La Trobe Institute for Sustainable Agriculture & Food, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Antony Bacic
- La Trobe Institute for Sustainable Agriculture & Food, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Monika S Doblin
- La Trobe Institute for Sustainable Agriculture & Food, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria 3086, Australia
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Yin L, Zander M, Huang SSC, Xie M, Song L, Saldierna Guzmán JP, Hann E, Shanbhag BK, Ng S, Jain S, Janssen BJ, Clark NM, Walley JW, Beddoe T, Bar-Joseph Z, Lewsey MG, Ecker JR. Transcription Factor Dynamics in Cross-Regulation of Plant Hormone Signaling Pathways. bioRxiv 2023:2023.03.07.531630. [PMID: 36945593 PMCID: PMC10028877 DOI: 10.1101/2023.03.07.531630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Cross-regulation between hormone signaling pathways is indispensable for plant growth and development. However, the molecular mechanisms by which multiple hormones interact and co-ordinate activity need to be understood. Here, we generated a cross-regulation network explaining how hormone signals are integrated from multiple pathways in etiolated Arabidopsis (Arabidopsis thaliana) seedlings. To do so we comprehensively characterized transcription factor activity during plant hormone responses and reconstructed dynamic transcriptional regulatory models for six hormones; abscisic acid, brassinosteroid, ethylene, jasmonic acid, salicylic acid and strigolactone/karrikin. These models incorporated target data for hundreds of transcription factors and thousands of protein-protein interactions. Each hormone recruited different combinations of transcription factors, a subset of which were shared between hormones. Hub target genes existed within hormone transcriptional networks, exhibiting transcription factor activity themselves. In addition, a group of MITOGEN-ACTIVATED PROTEIN KINASES (MPKs) were identified as potential key points of cross-regulation between multiple hormones. Accordingly, the loss of function of one of these (MPK6) disrupted the global proteome, phosphoproteome and transcriptome during hormone responses. Lastly, we determined that all hormones drive substantial alternative splicing that has distinct effects on the transcriptome compared with differential gene expression, acting in early hormone responses. These results provide a comprehensive understanding of the common features of plant transcriptional regulatory pathways and how cross-regulation between hormones acts upon gene expression.
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Affiliation(s)
- Lingling Yin
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, School of Agriculture Biomedicine and Environment, AgriBio Building, La Trobe University, Melbourne, VIC 3086, Australia
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
| | - Mark Zander
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Present address: Waksman Institute of Microbiology, Department of Plant Biology, Rutgers, The State University of New Jersey, NJ 08854, USA
| | - Shao-shan Carol Huang
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Present address: Department of Biology, New York University, New York, NY 10003, USA
| | - Mingtang Xie
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Present address: Cibus, San Diego, CA 92121, USA
| | - Liang Song
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Present address: Department of Botany, The University of British Columbia, Vancouver, British Columbia, Canada
| | - J. Paola Saldierna Guzmán
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Present address: Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Elizabeth Hann
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Present address: Department of Chemical and Environmental Engineering, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Bhuvana K. Shanbhag
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, School of Agriculture Biomedicine and Environment, AgriBio Building, La Trobe University, Melbourne, VIC 3086, Australia
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
| | - Sophia Ng
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, School of Agriculture Biomedicine and Environment, AgriBio Building, La Trobe University, Melbourne, VIC 3086, Australia
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
| | - Siddhartha Jain
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Bart J. Janssen
- The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
| | - Natalie M. Clark
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA, 50011 USA
| | - Justin W. Walley
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA, 50011 USA
| | - Travis Beddoe
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, School of Agriculture Biomedicine and Environment, AgriBio Building, La Trobe University, Melbourne, VIC 3086, Australia
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
| | - Ziv Bar-Joseph
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Mathew G. Lewsey
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, School of Agriculture Biomedicine and Environment, AgriBio Building, La Trobe University, Melbourne, VIC 3086, Australia
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
- Australian Research Council Centre of Excellence in Plants For Space, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
| | - Joseph R. Ecker
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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4
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Clark NM, Hurgobin B, Kelley DR, Lewsey MG, Walley JW. A Practical Guide to Inferring Multi-Omics Networks in Plant Systems. Methods Mol Biol 2023; 2698:233-257. [PMID: 37682479 DOI: 10.1007/978-1-0716-3354-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
The inference of gene regulatory networks can reveal molecular connections underlying biological processes and improve our understanding of complex biological phenomena in plants. Many previous network studies have inferred networks using only one type of omics data, such as transcriptomics. However, given more recent work applying multi-omics integration in plant biology, such as combining (phospho)proteomics with transcriptomics, it may be advantageous to integrate multiple omics data types into a comprehensive network prediction. Here, we describe a state-of-the-art approach for integrating multi-omics data with gene regulatory network inference to describe signaling pathways and uncover novel regulators. We detail how to download and process transcriptomics and (phospho)proteomics data for network inference, using an example dataset from the plant hormone signaling field. We provide a step-by-step protocol for inference, visualization, and analysis of an integrative multi-omics network using currently available methods. This chapter serves as an accessible guide for novice and intermediate bioinformaticians to analyze their own datasets and reanalyze published work.
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Affiliation(s)
- Natalie M Clark
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Bhavna Hurgobin
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, Bundoora, VIC, Australia
- La Trobe Institute for Sustainable Agriculture and Food, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia
| | - Dior R Kelley
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Mathew G Lewsey
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, Bundoora, VIC, Australia
- La Trobe Institute for Sustainable Agriculture and Food, Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC, Australia
- Australian Research Council Centre of Excellence in Plants for Space, AgriBio Building, La Trobe University, Bundoora, VIC, Australia
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
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5
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Conneely LJ, Berkowitz O, Lewsey MG. Emerging trends in genomic and epigenomic regulation of plant specialised metabolism. Phytochemistry 2022; 203:113427. [PMID: 36087823 DOI: 10.1016/j.phytochem.2022.113427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 08/23/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Regulation of specialised metabolism genes is multilayered and complex, influenced by an array of genomic, epigenetic and epigenomic mechanisms. Here, we review the most recent knowledge in this field, drawing from discoveries in several plant species. Our aim is to improve understanding of how plant genome structure and function influence specialised metabolism. We also highlight key areas for future exploration. Gene regulatory mechanisms influencing specialised metabolism include gene duplication and neo-functionalization, conservation of operon-like clusters of specialised metabolism genes, local chromatin modifications, and the organisation of higher order chromatin structures within the nucleus. Genomic and epigenomic research to-date in the discipline have focused on a relatively small number of plant species, primarily at whole organ or tissue level. This is largely due to the technical demands of the experimental methods needed. However, a high degree of cell-type specificity of function exists in specialised metabolism, driven by similarly specific gene regulation. In this review we focus on the genomic characteristics of genes that are found in different types of clusters within the genome. We propose that acquisition of cell-resolution epigenomic datasets in emerging models, such as the glandular trichomes of Cannabis sativa, will yield important advances. Data such as chromatin accessibility and histone modification profiles can pinpoint which regulatory sequences are active in individual cell types and at specific times in development. These could provide fundamental biological insight as well as novel targets for genetic engineering and crop improvement.
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Affiliation(s)
- Lee J Conneely
- La Trobe Institute for Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia; Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
| | - Oliver Berkowitz
- La Trobe Institute for Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia; Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
| | - Mathew G Lewsey
- La Trobe Institute for Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia; Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia.
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6
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He C, Liew LC, Yin L, Lewsey MG, Whelan J, Berkowitz O. The retrograde signaling regulator ANAC017 recruits the MKK9-MPK3/6, ethylene, and auxin signaling pathways to balance mitochondrial dysfunction with growth. Plant Cell 2022; 34:3460-3481. [PMID: 35708648 PMCID: PMC9421482 DOI: 10.1093/plcell/koac177] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 05/29/2022] [Indexed: 05/12/2023]
Abstract
In plant cells, mitochondria are ideally positioned to sense and balance changes in energy metabolism in response to changing environmental conditions. Retrograde signaling from mitochondria to the nucleus is crucial for adjusting the required transcriptional responses. We show that ANAC017, the master regulator of mitochondrial stress, directly recruits a signaling cascade involving the plant hormones ethylene and auxin as well as the MAP KINASE KINASE (MKK) 9-MAP KINASE (MPK) 3/6 pathway in Arabidopsis thaliana. Chromatin immunoprecipitation followed by sequencing and overexpression demonstrated that ANAC017 directly regulates several genes of the ethylene and auxin pathways, including MKK9, 1-AMINO-CYCLOPROPANE-1-CARBOXYLATE SYNTHASE 2, and YUCCA 5, in addition to genes encoding transcription factors regulating plant growth and stress responses such as BASIC REGION/LEUCINE ZIPPER MOTIF (bZIP) 60, bZIP53, ANAC081/ATAF2, and RADICAL-INDUCED CELL DEATH1. A time-resolved RNA-seq experiment established that ethylene signaling precedes the stimulation of auxin signaling in the mitochondrial stress response, with a large part of the transcriptional regulation dependent on ETHYLENE-INSENSITIVE 3. These results were confirmed by mutant analyses. Our findings identify the molecular components controlled by ANAC017, which integrates the primary stress responses to mitochondrial dysfunction with whole plant growth via the activation of regulatory and partly antagonistic feedback loops.
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Affiliation(s)
- Cunman He
- Department of Animal, Plant and Soil Science, La Trobe University, Bundoora, Victoria 3086, Australia
- ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Lim Chee Liew
- Department of Animal, Plant and Soil Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Lingling Yin
- Department of Animal, Plant and Soil Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Mathew G Lewsey
- Department of Animal, Plant and Soil Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - James Whelan
- Department of Animal, Plant and Soil Science, La Trobe University, Bundoora, Victoria 3086, Australia
- ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia
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Lewsey MG, Yi C, Berkowitz O, Ayora F, Bernado M, Whelan J. scCloudMine: A cloud-based app for visualization, comparison, and exploration of single-cell transcriptomic data. Plant Commun 2022; 3:100302. [PMID: 35605202 PMCID: PMC9284053 DOI: 10.1016/j.xplc.2022.100302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/13/2021] [Accepted: 01/20/2022] [Indexed: 06/12/2023]
Abstract
scCloudMine is a cloud-based application for visualization, comparison, and exploration of single-cell transcriptome data. It does not require an on-site, high-power computing server, installation, or associated expertise and expense. Users upload their own or publicly available scRNA-seq datasets after pre-processing for visualization using a web browser. The data can be viewed in two color modes-Cluster, representing cell identity, and Values, showing levels of expression-and data can be queried using keywords or gene identification number(s). Using the app to compare studies, we determined that some genes frequently used as cell-type markers are in fact study specific. The apparent cell-specific expression of PHO1;H3 differed between GFP-tagging and scRNA-seq studies. Some phosphate transporter genes were induced by protoplasting, but they retained cell specificity, suggesting that cell-specific responses to stress (i.e., protoplasting) can occur. Examination of the cell specificity of hormone response genes revealed that 132 hormone-responsive genes display restricted expression and that the jasmonate response gene TIFY8 is expressed in endodermal cells, in contrast to previous reports. It also appears that JAZ repressors have cell-type-specific functions. These features identified using scCloudMine highlight the need for resources to enable biological researchers to compare their datasets of interest under a variety of parameters. scCloudMine enables researchers to form new hypotheses and perform comparative studies and allows for the easy re-use of data from this emerging technology by a wide variety of users who may not have access or funding for high-performance on-site computing and support.
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Affiliation(s)
- Mathew G Lewsey
- La Trobe Institute for Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC 3086, Australia; Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC 3086, Australia
| | - Changyu Yi
- La Trobe Institute for Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC 3086, Australia
| | - Oliver Berkowitz
- La Trobe Institute for Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC 3086, Australia; Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC 3086, Australia
| | - Felipe Ayora
- BizData, Level 9/278, Collins Street, Melbourne, VIC 3000, Australia; Research and Advanced Computing, BizData, Level 31, 2-6, Gilmer Terrace, Wellington, 6011, New Zealand.
| | - Maurice Bernado
- BizData, Level 9/278, Collins Street, Melbourne, VIC 3000, Australia
| | - James Whelan
- La Trobe Institute for Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC 3086, Australia; Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC 3086, Australia; Department of Animal, Plant and Soil Sciences, School of Life Science, La Trobe University, Bundoora, VIC 3086, Australia.
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8
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Sarić R, Nguyen VD, Burge T, Berkowitz O, Trtílek M, Whelan J, Lewsey MG, Čustović E. Applications of hyperspectral imaging in plant phenotyping. Trends Plant Sci 2022; 27:301-315. [PMID: 34998690 DOI: 10.1016/j.tplants.2021.12.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 11/30/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Our ability to interrogate and manipulate the genome far exceeds our capacity to measure the effects of genetic changes on plant traits. Much effort has been made recently by the plant science research community to address this imbalance. The responses of plants to environmental conditions can now be defined using a variety of imaging approaches. Hyperspectral imaging (HSI) has emerged as a promising approach to measure traits using a wide range of wavebands simultaneously in 3D to capture information in lab, glasshouse, or field settings. HSI has been applied to define abiotic, biotic, and quality traits for optimisation of crop management.
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Affiliation(s)
- Rijad Sarić
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia; Department of Engineering, School of Engineering and Mathematical Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Viet D Nguyen
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia; Department of Engineering, School of Engineering and Mathematical Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Timothy Burge
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
| | - Martin Trtílek
- Photon Systems Instruments plant phenotyping research centre, Photon System Instruments, 664 24 Drasov, Brno, Czech Republic
| | - James Whelan
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia.
| | - Mathew G Lewsey
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
| | - Edhem Čustović
- Department of Engineering, School of Engineering and Mathematical Sciences, La Trobe University, Bundoora, VIC 3086, Australia
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9
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Nguyen VD, Sarić R, Burge T, Berkowitz O, Trtilek M, Whelan J, Lewsey MG, Čustović E. Noninvasive imaging technologies in plant phenotyping. Trends Plant Sci 2022; 27:316-317. [PMID: 34257004 DOI: 10.1016/j.tplants.2021.06.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/09/2021] [Accepted: 06/17/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Viet D Nguyen
- Department of Animal, Plant, and Soil Science, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia; Department of Engineering, School of Engineering and Mathematical Sciences, La Trobe University, Bundoora, VIC 3086, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
| | - Rijad Sarić
- Department of Animal, Plant, and Soil Science, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia; Department of Engineering, School of Engineering and Mathematical Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Timothy Burge
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant, and Soil Science, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
| | - Martin Trtilek
- Photon Systems Instruments plant phenotyping research centre, Photon System Instruments, 664 24 Drasov, Brno, Czech Republic
| | - James Whelan
- Department of Animal, Plant, and Soil Science, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia.
| | - Mathew G Lewsey
- Department of Animal, Plant, and Soil Science, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
| | - Edhem Čustović
- Department of Engineering, School of Engineering and Mathematical Sciences, La Trobe University, Bundoora, VIC 3086, Australia
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10
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Meng X, Li L, De Clercq I, Narsai R, Xu Y, Hartmann A, Claros DL, Custovic E, Lewsey MG, Whelan J, Berkowitz O. Corrigendum to: ANAC017 Coordinates Organellar Functions and Stress Responses by Reprogramming Retrograde Signaling. Plant Physiol 2021; 187:1026. [PMID: 34608973 PMCID: PMC8491010 DOI: 10.1093/plphys/kiab331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
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11
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Berkowitz O, Xu Y, Liew LC, Wang Y, Zhu Y, Hurgobin B, Lewsey MG, Whelan J. RNA-seq analysis of laser microdissected Arabidopsis thaliana leaf epidermis, mesophyll and vasculature defines tissue-specific transcriptional responses to multiple stress treatments. Plant J 2021; 107:938-955. [PMID: 33974297 DOI: 10.1111/tpj.15314] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/28/2021] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
Acclimation of plants to adverse conditions requires the coordination of gene expression and signalling pathways between tissues and cell types. As the energy and carbon capturing organs, leaves are significantly affected by abiotic and biotic stresses. However, tissue- or cell type-specific analyses of stress responses have focussed on the Arabidopsis root. Here, we comparatively explore the transcriptomes of three leaf tissues (epidermis, mesophyll, vasculature) after induction of diverse stress pathways by chemical stimuli (antimycin A, 3-amino-1,2,4-triazole, methyl viologen, salicylic acid) and ultraviolet light in Arabidopsis using laser capture microdissection followed by RNA sequencing. Stimulation of stress pathways caused an overall reduction in the number of genes expressed in a tissue-specific manner, though a small subset gained or changed their tissue specificity. We find no evidence of a common stress response, with only a few genes consistently responsive to two or more treatments in the analysed tissues. However, differentially expressed genes overlap between tissues for individual treatments. A focussed analysis provided evidence for an interaction of auxin and ethylene that mediates retrograde signalling during mitochondrial dysfunction specifically in the epidermis, and a gene regulatory network defined the hierarchy of interactions. Taken together, we have generated an extensive reference dataset that will be valuable for future experiments analysing transcriptional responses on a tissue or single-cell level. Our results will enable the tailoring of the tissue-specific engineering of stress-tolerant plants.
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Affiliation(s)
- Oliver Berkowitz
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Yue Xu
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Lim Chee Liew
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Yan Wang
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Yanqiao Zhu
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Bhavna Hurgobin
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Mathew G Lewsey
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - James Whelan
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
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12
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Hurgobin B, Tamiru‐Oli M, Welling MT, Doblin MS, Bacic A, Whelan J, Lewsey MG. Recent advances in Cannabis sativa genomics research. New Phytol 2021; 230:73-89. [PMID: 33283274 PMCID: PMC7986631 DOI: 10.1111/nph.17140] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/27/2020] [Indexed: 05/06/2023]
Abstract
Cannabis (Cannabis sativa L.) is one of the oldest cultivated plants purported to have unique medicinal properties. However, scientific research of cannabis has been restricted by the Single Convention on Narcotic Drugs of 1961, an international treaty that prohibits the production and supply of narcotic drugs except under license. Legislation governing cannabis cultivation for research, medicinal and even recreational purposes has been relaxed recently in certain jurisdictions. As a result, there is now potential to accelerate cultivar development of this multi-use and potentially medically useful plant species by application of modern genomics technologies. Whilst genomics has been pivotal to our understanding of the basic biology and molecular mechanisms controlling key traits in several crop species, much work is needed for cannabis. In this review we provide a comprehensive summary of key cannabis genomics resources and their applications. We also discuss prospective applications of existing and emerging genomics technologies for accelerating the genetic improvement of cannabis.
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Affiliation(s)
- Bhavna Hurgobin
- La Trobe Institute for Agriculture and FoodDepartment of Animal, Plant and Soil SciencesSchool of Life SciencesLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
- Australian Research Council Research Hub for Medicinal AgricultureLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
| | - Muluneh Tamiru‐Oli
- La Trobe Institute for Agriculture and FoodDepartment of Animal, Plant and Soil SciencesSchool of Life SciencesLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
- Australian Research Council Research Hub for Medicinal AgricultureLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
| | - Matthew T. Welling
- La Trobe Institute for Agriculture and FoodDepartment of Animal, Plant and Soil SciencesSchool of Life SciencesLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
- Australian Research Council Research Hub for Medicinal AgricultureLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
| | - Monika S. Doblin
- La Trobe Institute for Agriculture and FoodDepartment of Animal, Plant and Soil SciencesSchool of Life SciencesLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
- Australian Research Council Research Hub for Medicinal AgricultureLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
| | - Antony Bacic
- La Trobe Institute for Agriculture and FoodDepartment of Animal, Plant and Soil SciencesSchool of Life SciencesLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
- Australian Research Council Research Hub for Medicinal AgricultureLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
| | - James Whelan
- La Trobe Institute for Agriculture and FoodDepartment of Animal, Plant and Soil SciencesSchool of Life SciencesLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
- Australian Research Council Research Hub for Medicinal AgricultureLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
- Australian Research Council Centre of Excellence for Plant Energy BiologyLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
| | - Mathew G. Lewsey
- La Trobe Institute for Agriculture and FoodDepartment of Animal, Plant and Soil SciencesSchool of Life SciencesLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
- Australian Research Council Research Hub for Medicinal AgricultureLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
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13
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Affiliation(s)
- Quentin Gouil
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia.
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
| | - Mathew G Lewsey
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Bundoora, Victoria, Australia.
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, Bundoora, Victoria, Australia.
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14
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Sun S, Yi C, Ma J, Wang S, Peirats-Llobet M, Lewsey MG, Whelan J, Shou H. Analysis of Spatio-Temporal Transcriptome Profiles of Soybean ( Glycine max) Tissues during Early Seed Development. Int J Mol Sci 2020; 21:E7603. [PMID: 33066688 PMCID: PMC7589660 DOI: 10.3390/ijms21207603] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/11/2020] [Accepted: 10/13/2020] [Indexed: 01/17/2023] Open
Abstract
Soybean (Glycine max) is an important crop providing oil and protein for both human and animal consumption. Knowing which biological processes take place in specific tissues in a temporal manner will enable directed breeding or synthetic approaches to improve seed quantity and quality. We analyzed a genome-wide transcriptome dataset from embryo, endosperm, endothelium, epidermis, hilum, outer and inner integument and suspensor at the global, heart and cotyledon stages of soybean seed development. The tissue specificity of gene expression was greater than stage specificity, and only three genes were differentially expressed in all seed tissues. Tissues had both unique and shared enriched functional categories of tissue-specifically expressed genes associated with them. Strong spatio-temporal correlation in gene expression was identified using weighted gene co-expression network analysis, with the most co-expression occurring in one seed tissue. Transcription factors with distinct spatiotemporal gene expression programs in each seed tissue were identified as candidate regulators of expression within those tissues. Gene ontology (GO) enrichment of orthogroup clusters revealed the conserved functions and unique roles of orthogroups with similar and contrasting expression patterns in transcript abundance between soybean and Arabidopsis during embryo proper and endosperm development. Key regulators in each seed tissue and hub genes connecting those networks were characterized by constructing gene regulatory networks. Our findings provide an important resource for describing the structure and function of individual soybean seed compartments during early seed development.
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Affiliation(s)
- Shuo Sun
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; (S.S.); (J.M.)
| | - Changyu Yi
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia; (C.Y.); (M.P.-L.)
| | - Jing Ma
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; (S.S.); (J.M.)
| | - Shoudong Wang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun 130102, China;
| | - Marta Peirats-Llobet
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia; (C.Y.); (M.P.-L.)
| | - Mathew G. Lewsey
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Victoria 3086, Australia;
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Victoria 3086, Australia
| | - James Whelan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; (S.S.); (J.M.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia; (C.Y.); (M.P.-L.)
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Huixia Shou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; (S.S.); (J.M.)
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15
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Lozano-Claros D, Meng X, Custovic E, Deng G, Berkowitz O, Whelan J, Lewsey MG. Developmental normalization of phenomics data generated by high throughput plant phenotyping systems. Plant Methods 2020; 16:111. [PMID: 32817754 PMCID: PMC7424680 DOI: 10.1186/s13007-020-00653-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/06/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Sowing time is commonly used as the temporal reference for Arabidopsis thaliana (Arabidopsis) experiments in high throughput plant phenotyping (HTPP) systems. This relies on the assumption that germination and seedling establishment are uniform across the population. However, individual seeds have different development trajectories even under uniform environmental conditions. This leads to increased variance in quantitative phenotyping approaches. We developed the Digital Adjustment of Plant Development (DAPD) normalization method. It normalizes time-series HTPP measurements by reference to an early developmental stage and in an automated manner. The timeline of each measurement series is shifted to a reference time. The normalization is determined by cross-correlation at multiple time points of the time-series measurements, which may include rosette area, leaf size, and number. RESULTS The DAPD method improved the accuracy of phenotyping measurements by decreasing the statistical dispersion of quantitative traits across a time-series. We applied DAPD to evaluate the relative growth rate in Arabidopsis plants and demonstrated that it improves uniformity in measurements, permitting a more informative comparison between individuals. Application of DAPD decreased variance of phenotyping measurements by up to 2.5 times compared to sowing-time normalization. The DAPD method also identified more outliers than any other central tendency technique applied to the non-normalized dataset. CONCLUSIONS DAPD is an effective method to control for temporal differences in development within plant phenotyping datasets. In principle, it can be applied to HTPP data from any species/trait combination for which a relevant developmental scale can be defined.
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Affiliation(s)
- Diego Lozano-Claros
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, VIC 3086 Australia
- Department of Engineering, School of Engineering and Mathematical Sciences, La Trobe University, Melbourne, VIC 3086 Australia
| | - Xiangxiang Meng
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, VIC 3086 Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, VIC 3086 Australia
- Currently: Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Eddie Custovic
- Department of Engineering, School of Engineering and Mathematical Sciences, La Trobe University, Melbourne, VIC 3086 Australia
| | - Guang Deng
- Department of Engineering, School of Engineering and Mathematical Sciences, La Trobe University, Melbourne, VIC 3086 Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, VIC 3086 Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086 Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, VIC 3086 Australia
| | - James Whelan
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, VIC 3086 Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086 Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, VIC 3086 Australia
| | - Mathew G. Lewsey
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, VIC 3086 Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086 Australia
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16
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Liew LC, Wang Y, Peirats-Llobet M, Berkowitz O, Whelan J, Lewsey MG. Laser-Capture Microdissection RNA-Sequencing for Spatial and Temporal Tissue-Specific Gene Expression Analysis in Plants. J Vis Exp 2020. [PMID: 32831315 DOI: 10.3791/61517] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The development of a complex multicellular organism is governed by distinct cell types that have different transcriptional profiles. To identify transcriptional regulatory networks that govern developmental processes it is necessary to measure the spatial and temporal gene expression profiles of these individual cell types. Therefore, insight into the spatio-temporal control of gene expression is essential to gain understanding of how biological and developmental processes are regulated. Here, we describe a laser-capture microdissection (LCM) method to isolate small number of cells from three barley embryo organs over a time-course during germination followed by transcript profiling. The method consists of tissue fixation, tissue processing, paraffin embedding, sectioning, LCM and RNA extraction followed by real-time PCR or RNA-seq. This method has enabled us to obtain spatial and temporal profiles of seed organ transcriptomes from varying numbers of cells (tens to hundreds), providing much greater tissue-specificity than typical bulk-tissue analyses. From these data we were able to define and compare transcriptional regulatory networks as well as predict candidate regulatory transcription factors for individual tissues. The method should be applicable to other plant tissues with minimal optimization.
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Affiliation(s)
- Lim Chee Liew
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University; Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University
| | - Yan Wang
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University; Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University
| | - Marta Peirats-Llobet
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University; Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University
| | - James Whelan
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University; Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University
| | - Mathew G Lewsey
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University;
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17
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Zander M, Lewsey MG, Clark NM, Yin L, Bartlett A, Saldierna Guzmán JP, Hann E, Langford AE, Jow B, Wise A, Nery JR, Chen H, Bar-Joseph Z, Walley JW, Solano R, Ecker JR. Publisher Correction: Integrated multi-omics framework of the plant response to jasmonic acid. Nat Plants 2020; 6:1065. [PMID: 32694625 DOI: 10.1038/s41477-020-0743-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Mark Zander
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Mathew G Lewsey
- Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, Victoria, Australia.
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, Centre for AgriBioscience, La Trobe University, Bundoora, Victoria, Australia.
| | - Natalie M Clark
- Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Lingling Yin
- Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, Victoria, Australia
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, Centre for AgriBioscience, La Trobe University, Bundoora, Victoria, Australia
| | - Anna Bartlett
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - J Paola Saldierna Guzmán
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- School of Natural Sciences, University of California Merced, Merced, CA, USA
| | - Elizabeth Hann
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Chemical and Environmental Engineering, Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Amber E Langford
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Bruce Jow
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Aaron Wise
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Huaming Chen
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ziv Bar-Joseph
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Justin W Walley
- Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Roberto Solano
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Joseph R Ecker
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, USA.
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18
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Ortigosa A, Fonseca S, Franco-Zorrilla JM, Fernández-Calvo P, Zander M, Lewsey MG, García-Casado G, Fernández-Barbero G, Ecker JR, Solano R. The JA-pathway MYC transcription factors regulate photomorphogenic responses by targeting HY5 gene expression. Plant J 2020; 102:138-152. [PMID: 31755159 DOI: 10.1111/tpj.14618] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/28/2019] [Accepted: 11/05/2019] [Indexed: 05/18/2023]
Abstract
Jasmonates are key regulators of the balance between defence and growth in plants. However, the molecular mechanisms by which activation of defence reduces growth are not yet fully understood. Here, we analyze the role of MYC transcription factors (TFs) and jasmonic acid (JA) in photomorphogenic growth. We found that multiple myc mutants share light-associated phenotypes with mutants of the phytochrome B photoreceptor, such as delayed seed germination in the dark and long hypocotyl growth. Overexpression of MYC2 in a phyB background partially suppressed its long hypocotyl phenotype. Transcriptomic analysis of multiple myc mutants confirmed that MYCs are required for full expression of red (R) light-regulated genes, including the master regulator HY5. ChIP-seq analyses revealed that MYC2 and MYC3 bind directly to the promoter of HY5 and that HY5 gene expression and protein levels are compromised in multiple myc mutants. Altogether, our results pinpoint MYCs as photomorphogenic TFs that control phytochrome responses by activating HY5 expression. This has important implications in understanding the trade-off between growth and defence as the same TFs that activate defence responses are photomorphogenic growth regulators.
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Affiliation(s)
- Andrés Ortigosa
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049, Madrid, Spain
| | - Sandra Fonseca
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049, Madrid, Spain
| | - José M Franco-Zorrilla
- Genomics Unit, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049, Madrid, Spain
| | - Patricia Fernández-Calvo
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049, Madrid, Spain
| | - Mark Zander
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Mathew G Lewsey
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, Centre for AgriBioscience, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
| | - Gloria García-Casado
- Genomics Unit, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049, Madrid, Spain
| | - Gemma Fernández-Barbero
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049, Madrid, Spain
| | - Joseph R Ecker
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Roberto Solano
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049, Madrid, Spain
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19
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Zander M, Lewsey MG, Clark NM, Yin L, Bartlett A, Saldierna Guzmán JP, Hann E, Langford AE, Jow B, Wise A, Nery JR, Chen H, Bar-Joseph Z, Walley JW, Solano R, Ecker JR. Integrated multi-omics framework of the plant response to jasmonic acid. Nat Plants 2020; 6:290-302. [PMID: 32170290 PMCID: PMC7094030 DOI: 10.1038/s41477-020-0605-7] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/23/2020] [Indexed: 05/17/2023]
Abstract
Understanding the systems-level actions of transcriptional responses to hormones provides insight into how the genome is reprogrammed in response to environmental stimuli. Here, we investigated the signalling pathway of the hormone jasmonic acid (JA), which controls a plethora of critically important processes in plants and is orchestrated by the transcription factor MYC2 and its closest relatives in Arabidopsis thaliana. We generated an integrated framework of the response to JA, which spans from the activity of master and secondary regulatory transcription factors, through gene expression outputs and alternative splicing, to protein abundance changes, protein phosphorylation and chromatin remodelling. We integrated time-series transcriptome analysis with (phospho)proteomic data to reconstruct gene regulatory network models. These enabled us to predict previously unknown points of crosstalk of JA to other signalling pathways and to identify new components of the JA regulatory mechanism, which we validated through targeted mutant analysis. These results provide a comprehensive understanding of how a plant hormone remodels cellular functions and plant behaviour, the general principles of which provide a framework for analyses of cross-regulation between other hormone and stress signalling pathways.
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Affiliation(s)
- Mark Zander
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Mathew G Lewsey
- Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, Victoria, Australia.
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, Centre for AgriBioscience, La Trobe University, Bundoora, Victoria, Australia.
| | - Natalie M Clark
- Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Lingling Yin
- Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, Victoria, Australia
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, Centre for AgriBioscience, La Trobe University, Bundoora, Victoria, Australia
| | - Anna Bartlett
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - J Paola Saldierna Guzmán
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- School of Natural Sciences, University of California Merced, Merced, CA, USA
| | - Elizabeth Hann
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Chemical and Environmental Engineering, Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Amber E Langford
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Bruce Jow
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Aaron Wise
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Huaming Chen
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ziv Bar-Joseph
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Justin W Walley
- Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Roberto Solano
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Joseph R Ecker
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, USA.
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20
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Zander M, Lewsey MG, Clark NM, Yin L, Bartlett A, Saldierna Guzmán JP, Hann E, Langford AE, Jow B, Wise A, Nery JR, Chen H, Bar-Joseph Z, Walley JW, Solano R, Ecker JR. Integrated multi-omics framework of the plant response to jasmonic acid. Nat Plants 2020; 6:290-302. [PMID: 32170290 DOI: 10.1038/s41477-020-0605-607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/23/2020] [Indexed: 05/26/2023]
Abstract
Understanding the systems-level actions of transcriptional responses to hormones provides insight into how the genome is reprogrammed in response to environmental stimuli. Here, we investigated the signalling pathway of the hormone jasmonic acid (JA), which controls a plethora of critically important processes in plants and is orchestrated by the transcription factor MYC2 and its closest relatives in Arabidopsis thaliana. We generated an integrated framework of the response to JA, which spans from the activity of master and secondary regulatory transcription factors, through gene expression outputs and alternative splicing, to protein abundance changes, protein phosphorylation and chromatin remodelling. We integrated time-series transcriptome analysis with (phospho)proteomic data to reconstruct gene regulatory network models. These enabled us to predict previously unknown points of crosstalk of JA to other signalling pathways and to identify new components of the JA regulatory mechanism, which we validated through targeted mutant analysis. These results provide a comprehensive understanding of how a plant hormone remodels cellular functions and plant behaviour, the general principles of which provide a framework for analyses of cross-regulation between other hormone and stress signalling pathways.
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Affiliation(s)
- Mark Zander
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Mathew G Lewsey
- Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, Victoria, Australia.
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, Centre for AgriBioscience, La Trobe University, Bundoora, Victoria, Australia.
| | - Natalie M Clark
- Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Lingling Yin
- Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, Victoria, Australia
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, Centre for AgriBioscience, La Trobe University, Bundoora, Victoria, Australia
| | - Anna Bartlett
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - J Paola Saldierna Guzmán
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- School of Natural Sciences, University of California Merced, Merced, CA, USA
| | - Elizabeth Hann
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Chemical and Environmental Engineering, Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Amber E Langford
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Bruce Jow
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Aaron Wise
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Huaming Chen
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ziv Bar-Joseph
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Justin W Walley
- Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Roberto Solano
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Joseph R Ecker
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, USA.
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21
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Liew LC, Narsai R, Wang Y, Berkowitz O, Whelan J, Lewsey MG. Temporal tissue-specific regulation of transcriptomes during barley (Hordeum vulgare) seed germination. Plant J 2020; 101:700-715. [PMID: 31628689 DOI: 10.1111/tpj.14574] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 09/09/2019] [Accepted: 10/08/2019] [Indexed: 06/10/2023]
Abstract
The distinct functions of individual cell types require cells to express specific sets of genes. The germinating seed is an excellent model to study genome regulation between cell types since the majority of the transcriptome is differentially expressed in a short period, beginning from a uniform, metabolically inactive state. In this study, we applied laser-capture microdissection RNA-sequencing to small numbers of cells from the plumule, radicle tip and scutellum of germinating barley seeds every 8 h, over a 48 h time course. Tissue-specific gene expression was notably common; 25% (910) of differentially expressed transcripts in plumule, 34% (1876) in radicle tip and 41% (2562) in scutellum were exclusive to that organ. We also determined that tissue-specific storage of transcripts occurs during seed development and maturation. Co-expression of genes had strong spatiotemporal structure, with most co-expression occurring within one organ and at a subset of specific time points during germination. Overlapping and distinct enrichment of functional categories were observed in the tissue-specific profiles. We identified candidate transcription factors amongst these that may be regulators of spatiotemporal gene expression programs. Our findings contribute to the broader goal of generating an integrative model that describes the structure and function of individual cells within seeds during germination.
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Affiliation(s)
- Lim Chee Liew
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Vic., 3086, Australia
| | - Reena Narsai
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
| | - Yan Wang
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Vic., 3086, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
| | - James Whelan
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
| | - Mathew G Lewsey
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
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22
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Affiliation(s)
- Marta Peirats-Llobet
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
| | - Mathew G Lewsey
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, Centre for AgriBioscience, La Trobe University, Bundoora, Vic., 3086, Australia
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23
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Zander M, Willige BC, He Y, Nguyen TA, Langford AE, Nehring R, Howell E, McGrath R, Bartlett A, Castanon R, Nery JR, Chen H, Zhang Z, Jupe F, Stepanova A, Schmitz RJ, Lewsey MG, Chory J, Ecker JR. Epigenetic silencing of a multifunctional plant stress regulator. eLife 2019; 8:47835. [PMID: 31418686 PMCID: PMC6739875 DOI: 10.7554/elife.47835] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 08/15/2019] [Indexed: 12/30/2022] Open
Abstract
The central regulator of the ethylene (ET) signaling pathway, which controls a plethora of developmental programs and responses to environmental cues in plants, is ETHYLENE-INSENSITIVE2 (EIN2). Here we identify a chromatin-dependent regulatory mechanism at EIN2 requiring two genes: ETHYLENE-INSENSITIVE6 (EIN6), which is a H3K27me3 demethylase also known as RELATIVE OF EARLY FLOWERING6 (REF6), and EIN6 ENHANCER (EEN), the Arabidopsis homolog of the yeast INO80 chromatin remodeling complex subunit IES6 (INO EIGHTY SUBUNIT). Strikingly, EIN6 (REF6) and the INO80 complex redundantly control the level and the localization of the repressive histone modification H3K27me3 and the histone variant H2A.Z at the 5’ untranslated region (5’UTR) intron of EIN2. Concomitant loss of EIN6 (REF6) and the INO80 complex shifts the chromatin landscape at EIN2 to a repressive state causing a dramatic reduction of EIN2 expression. These results uncover a unique type of chromatin regulation which safeguards the expression of an essential multifunctional plant stress regulator.
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Affiliation(s)
- Mark Zander
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States.,Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, United States.,Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, United States
| | - Björn C Willige
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - Yupeng He
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - Thu A Nguyen
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - Amber E Langford
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - Ramlah Nehring
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - Elizabeth Howell
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - Robert McGrath
- Department of Biology, University of Pennsylvania, Philadelphia, United States
| | - Anna Bartlett
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - Rosa Castanon
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - Joseph R Nery
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - Huaming Chen
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - Zhuzhu Zhang
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - Florian Jupe
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - Anna Stepanova
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - Robert J Schmitz
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - Mathew G Lewsey
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - Joanne Chory
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States.,Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, United States
| | - Joseph R Ecker
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States.,Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, United States.,Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, United States
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24
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Meng X, Li L, De Clercq I, Narsai R, Xu Y, Hartmann A, Claros DL, Custovic E, Lewsey MG, Whelan J, Berkowitz O. ANAC017 Coordinates Organellar Functions and Stress Responses by Reprogramming Retrograde Signaling. Plant Physiol 2019; 180:634-653. [PMID: 30872424 PMCID: PMC6501098 DOI: 10.1104/pp.18.01603] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 03/08/2019] [Indexed: 05/17/2023]
Abstract
Mitochondria adjust their activities in response to external and internal stimuli to optimize growth via the mitochondrial retrograde response signaling pathway. The Arabidopsis (Arabidopsis thaliana) NAC domain transcription factor ANAC017 has previously been identified as a regulator of the mitochondrial retrograde response. We show here that overexpression of ANAC017 in Arabidopsis leads to growth retardation, altered leaf development with decreased cell size and viability, and early leaf senescence. RNA sequencing analyses revealed that increased ANAC017 expression leads to higher expression of genes related to mitochondrial stress, cell death/autophagy, and leaf senescence under nonlimiting growth conditions as well as extensive repression of chloroplast function. Gene regulatory network analysis indicated that a complex hierarchy of transcription factors exists downstream of ANAC017. These involve a set of up-regulated ANAC and WRKY transcription factors associated with organellar signaling and senescence. The network also includes a number of ethylene- and gibberellic acid-related transcription factors with established functions in stress responses and growth regulation, which down-regulate their target genes. A number of BASIC LEUCINE-ZIPPER MOTIF transcription factors involved in the endoplasmic reticulum unfolded protein response or balancing of energy homeostasis via the SNF1-RELATED PROTEIN KINASE1 were also down-regulated by ANAC017 overexpression. Our results show that the endoplasmic reticulum membrane tethering of the constitutively expressed ANAC017, and its controlled release, are crucial to fine-tune a fast reactive but potentially harmful signaling cascade. Thus, ANAC017 is a master regulator of cellular responses with mitochondria acting as central sensors.
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Affiliation(s)
- Xiangxiang Meng
- Department of Animal, Plant, and Soil Science, Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Lu Li
- Department of Animal, Plant, and Soil Science, Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Inge De Clercq
- Ghent University, Department of Plant Biotechnology and Bioinformatics, and VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Reena Narsai
- Department of Animal, Plant, and Soil Science, Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Yue Xu
- Department of Animal, Plant, and Soil Science, Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Andreas Hartmann
- Department of Animal, Plant, and Soil Science, Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Diego Lozano Claros
- Department of Animal, Plant, and Soil Science, Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Eddie Custovic
- School of Engineering and Mathematical Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Mathew G Lewsey
- Department of Animal, Plant, and Soil Science, Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia
| | - James Whelan
- Department of Animal, Plant, and Soil Science, Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant, and Soil Science, Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia
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25
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Robinson AJ, Tamiru M, Salby R, Bolitho C, Williams A, Huggard S, Fisch E, Unsworth K, Whelan J, Lewsey MG. AgriSeqDB: an online RNA-Seq database for functional studies of agriculturally relevant plant species. BMC Plant Biol 2018; 18:200. [PMID: 30231853 PMCID: PMC6146512 DOI: 10.1186/s12870-018-1406-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/30/2018] [Indexed: 05/12/2023]
Abstract
BACKGROUND The genome-wide expression profile of genes in different tissues/cell types and developmental stages is a vital component of many functional genomic studies. Transcriptome data obtained by RNA-sequencing (RNA-Seq) is often deposited in public databases that are made available via data portals. Data visualization is one of the first steps in assessment and hypothesis generation. However, these databases do not typically include visualization tools and establishing one is not trivial for users who are not computational experts. This, as well as the various formats in which data is commonly deposited, makes the processes of data access, sharing and utility more difficult. Our goal was to provide a simple and user-friendly repository that meets these needs for data-sets from major agricultural crops. DESCRIPTION AgriSeqDB ( https://expression.latrobe.edu.au/agriseqdb ) is a database for viewing, analysing and interpreting developmental and tissue/cell-specific transcriptome data from several species, including major agricultural crops such as wheat, rice, maize, barley and tomato. The disparate manner in which public transcriptome data is often warehoused and the challenge of visualizing raw data are both major hurdles to data reuse. The popular eFP browser does an excellent job of presenting transcriptome data in an easily interpretable view, but previous implementation has been mostly on a case-by-case basis. Here we present an integrated visualisation database of transcriptome data-sets from six species that did not previously have public-facing visualisations. We combine the eFP browser, for gene-by-gene investigation, with the Degust browser, which enables visualisation of all transcripts across multiple samples. The two visualisation interfaces launch from the same point, enabling users to easily switch between analysis modes. The tools allow users, even those without bioinformatics expertise, to mine into data-sets and understand the behaviour of transcripts of interest across samples and time. We have also incorporated an additional graphic download option to simplify incorporation into presentations or publications. CONCLUSION Powered by eFP and Degust browsers, AgriSeqDB is a quick and easy-to-use platform for data analysis and visualization in five crops and Arabidopsis. Furthermore, it provides a tool that makes it easy for researchers to share their data-sets, promoting research collaborations and data-set reuse.
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Affiliation(s)
| | - Muluneh Tamiru
- Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, Australia
| | - Rachel Salby
- Library, La Trobe University, Melbourne, Australia
| | | | | | | | - Eva Fisch
- Library, La Trobe University, Melbourne, Australia
| | | | - James Whelan
- Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, Australia
| | - Mathew G. Lewsey
- Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, Australia
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26
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Tamiru M, Hardcastle TJ, Lewsey MG. Regulation of genome-wide DNA methylation by mobile small RNAs. New Phytol 2018; 217:540-546. [PMID: 29105762 DOI: 10.1111/nph.14874] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 09/20/2017] [Indexed: 05/20/2023]
Abstract
Contents Summary 540 I. Introduction 540 II. There are different types of sRNA mobility 541 III. Mechanisms of sRNA movement 541 IV. Long-distance, shoot-root, mobile siRNAs influence DNA methylation in recipient tissues 541 V. Classes of interactions between shoot-root mobile siRNAs and DNA methylation 542 VI. Loci targeted directly and indirectly by shoot-root mobile siRNAs are associated with different histone modifications 543 VII. Is mobile siRNA-regulated DNA methylation important in specific tissues or under specific conditions? 543 VIII. Mobile sRNAs can be used to modify plant traits 544 IX. Conclusions 544 Acknowledgements 544 References 544 SUMMARY: RNA-directed DNA methylation (RdDM) at cytosine residues regulates gene expression, silences transposable elements and influences genome stability. The mechanisms responsible for RdDM are guided to target loci by small RNAs (sRNAs) that can move within plants cell to cell and long distance. Here we discuss recent advances in the understanding of interactions between mobile sRNAs and DNA methylation. We describe the mechanisms of sRNA movement, the differences between known classes of mobile sRNA-DNA methylation interactions and the limits of current knowledge. Finally, we discuss potential applications of mobile sRNAs in modifying plant traits.
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Affiliation(s)
- Muluneh Tamiru
- Centre for AgriBioscience, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Vic., 3086, Australia
| | - Thomas J Hardcastle
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Mathew G Lewsey
- Centre for AgriBioscience, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Vic., 3086, Australia
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27
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Narsai R, Gouil Q, Secco D, Srivastava A, Karpievitch YV, Liew LC, Lister R, Lewsey MG, Whelan J. Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination. Genome Biol 2017; 18:172. [PMID: 28911330 PMCID: PMC5599894 DOI: 10.1186/s13059-017-1302-3] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 08/16/2017] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Seed germination involves progression from complete metabolic dormancy to a highly active, growing seedling. Many factors regulate germination and these interact extensively, forming a complex network of inputs that control the seed-to-seedling transition. Our understanding of the direct regulation of gene expression and the dynamic changes in the epigenome and small RNAs during germination is limited. The interactions between genome, transcriptome and epigenome must be revealed in order to identify the regulatory mechanisms that control seed germination. RESULTS We present an integrated analysis of high-resolution RNA sequencing, small RNA sequencing and MethylC sequencing over ten developmental time points in Arabidopsis thaliana seeds, finding extensive transcriptomic and epigenomic transformations associated with seed germination. We identify previously unannotated loci from which messenger RNAs are expressed transiently during germination and find widespread alternative splicing and divergent isoform abundance of genes involved in RNA processing and splicing. We generate the first dynamic transcription factor network model of germination, identifying known and novel regulatory factors. Expression of both microRNA and short interfering RNA loci changes significantly during germination, particularly between the seed and the post-germinative seedling. These are associated with changes in gene expression and large-scale demethylation observed towards the end of germination, as the epigenome transitions from an embryo-like to a vegetative seedling state. CONCLUSIONS This study reveals the complex dynamics and interactions of the transcriptome and epigenome during seed germination, including the extensive remodelling of the seed DNA methylome from an embryo-like to vegetative-like state during the seed-to-seedling transition. Data are available for exploration in a user-friendly browser at https://jbrowse.latrobe.edu.au/germination_epigenome .
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Affiliation(s)
- Reena Narsai
- ARC Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.
- Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.
| | - Quentin Gouil
- Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia
| | - David Secco
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia
| | - Akanksha Srivastava
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia
| | - Yuliya V Karpievitch
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia
- Harry Perkins Institute of Medical Research, Perth, WA, 6009, Australia
| | - Lim Chee Liew
- Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Ryan Lister
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia
- Harry Perkins Institute of Medical Research, Perth, WA, 6009, Australia
| | - Mathew G Lewsey
- Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.
| | - James Whelan
- ARC Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia
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Gimenez-Ibanez S, Boter M, Ortigosa A, García-Casado G, Chini A, Lewsey MG, Ecker JR, Ntoukakis V, Solano R. JAZ2 controls stomata dynamics during bacterial invasion. New Phytol 2017; 213:1378-1392. [PMID: 28005270 DOI: 10.1111/nph.14354] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 10/17/2016] [Indexed: 05/21/2023]
Abstract
Coronatine (COR) facilitates entry of bacteria into the plant apoplast by stimulating stomata opening. COR-induced signaling events at stomata remain unclear. We found that the COR and jasmonate isoleucine (JA-Ile) co-receptor JAZ2 is constitutively expressed in guard cells and modulates stomatal dynamics during bacterial invasion We analyzed tissue expression patterns of AtJAZ genes and measured stomata opening and pathogen resistance in loss- and gain-of-function mutants. Arabidopsis jaz2 mutants are partially impaired in pathogen-induced stomatal closing and more susceptible to Pseudomonas. Gain-of-function mutations in JAZ2 prevent stomatal reopening by COR and are highly resistant to bacterial penetration. The JAZ2 targets MYC2, MYC3 and MYC4 directly regulate the expression of ANAC19, ANAC55 and ANAC72 to modulate stomata aperture. Due to the antagonistic interactions between the salicylic acid (SA) and JA defense pathways, efforts to increase resistance to biotrophs result in enhanced susceptibility to necrotrophs, and vice versa. Remarkably, dominant jaz2Δjas mutants are resistant to Pseudomonas syringae but retain unaltered resistance against necrotrophs. Our results demonstrate the existence of a COI1-JAZ2-MYC2,3,4-ANAC19,55,72 module responsible for the regulation of stomatal aperture that is hijacked by bacterial COR to promote infection. They also provide novel strategies for crop protection against biotrophs without compromising resistance to necrotrophs.
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Affiliation(s)
- Selena Gimenez-Ibanez
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC (CNB-CSIC), Madrid, 28049, Spain
| | - Marta Boter
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC (CNB-CSIC), Madrid, 28049, Spain
| | - Andrés Ortigosa
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC (CNB-CSIC), Madrid, 28049, Spain
| | - Gloria García-Casado
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC (CNB-CSIC), Madrid, 28049, Spain
| | - Andrea Chini
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC (CNB-CSIC), Madrid, 28049, Spain
| | - Mathew G Lewsey
- Centre for AgriBioscience, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Vardis Ntoukakis
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Roberto Solano
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC (CNB-CSIC), Madrid, 28049, Spain
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O'Malley RC, Huang SSC, Song L, Lewsey MG, Bartlett A, Nery JR, Galli M, Gallavotti A, Ecker JR. Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape. Cell 2016; 165:1280-1292. [PMID: 27203113 PMCID: PMC4907330 DOI: 10.1016/j.cell.2016.04.038] [Citation(s) in RCA: 736] [Impact Index Per Article: 92.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 02/26/2016] [Accepted: 04/11/2016] [Indexed: 10/21/2022]
Abstract
The cistrome is the complete set of transcription factor (TF) binding sites (cis-elements) in an organism, while an epicistrome incorporates tissue-specific DNA chemical modifications and TF-specific chemical sensitivities into these binding profiles. Robust methods to construct comprehensive cistrome and epicistrome maps are critical for elucidating complex transcriptional networks that underlie growth, behavior, and disease. Here, we describe DNA affinity purification sequencing (DAP-seq), a high-throughput TF binding site discovery method that interrogates genomic DNA with in-vitro-expressed TFs. Using DAP-seq, we defined the Arabidopsis cistrome by resolving motifs and peaks for 529 TFs. Because genomic DNA used in DAP-seq retains 5-methylcytosines, we determined that >75% (248/327) of Arabidopsis TFs surveyed were methylation sensitive, a property that strongly impacts the epicistrome landscape. DAP-seq datasets also yielded insight into the biology and binding site architecture of numerous TFs, demonstrating the value of DAP-seq for cost-effective cistromic and epicistromic annotation in any organism.
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Affiliation(s)
- Ronan C O'Malley
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA; Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Shao-Shan Carol Huang
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA; Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Liang Song
- Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Mathew G Lewsey
- Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Mary Galli
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA; Waksman Institute, Rutgers University, Piscataway, NJ 08854-8020, USA
| | - Andrea Gallavotti
- Waksman Institute, Rutgers University, Piscataway, NJ 08854-8020, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA; Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA.
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O’Malley RC, Huang SSC, Song L, Lewsey MG, Bartlett A, Nery JR, Galli M, Gallavotti A, Ecker JR. Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape. Cell 2016; 166:1598. [DOI: 10.1016/j.cell.2016.08.063] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
Small (s)RNAs of 21 to 24 nucleotides are associated with RNA silencing and methylation of DNA cytosine residues. All sizes can move from cell-to-cell and long distance in plants, directing RNA silencing in destination cells. Twenty-four nucleotide sRNAs are the predominant long-distance mobile species. Thousands move from shoot to root, where they target methylation of transposable elements both directly and indirectly. We derive several classes of interaction between small RNAs and methylation and use these to explore the mechanisms of methylation and gene expression that associate with mobile sRNA signaling.
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Affiliation(s)
| | - Mathew G Lewsey
- b Department of Animal, Plant and Soil Science, Center for AgriBioscience, School of Life Science , La Trobe University , Bundoora , Australia
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Lee WS, Fu SF, Li Z, Murphy AM, Dobson EA, Garland L, Chaluvadi SR, Lewsey MG, Nelson RS, Carr JP. Salicylic acid treatment and expression of an RNA-dependent RNA polymerase 1 transgene inhibit lethal symptoms and meristem invasion during tobacco mosaic virus infection in Nicotiana benthamiana. BMC Plant Biol 2016; 16:15. [PMID: 26757721 PMCID: PMC4710973 DOI: 10.1186/s12870-016-0705-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 01/06/2016] [Indexed: 05/23/2023]
Abstract
BACKGROUND Host RNA-dependent RNA polymerases (RDRs) 1 and 6 contribute to antiviral RNA silencing in plants. RDR6 is constitutively expressed and was previously shown to limit invasion of Nicotiana benthamiana meristem tissue by potato virus X and thereby inhibit disease development. RDR1 is inducible by salicylic acid (SA) and several other phytohormones. But although it contributes to basal resistance to tobacco mosaic virus (TMV) it is dispensable for SA-induced resistance in inoculated leaves. The laboratory accession of N. benthamiana is a natural rdr1 mutant and highly susceptible to TMV. However, TMV-induced symptoms are ameliorated in transgenic plants expressing Medicago truncatula RDR1. RESULTS In MtRDR1-transgenic N. benthamiana plants the spread of TMV expressing the green fluorescent protein (TMV.GFP) into upper, non-inoculated, leaves was not inhibited. However, in these plants exclusion of TMV.GFP from the apical meristem and adjacent stem tissue was greater than in control plants and this exclusion effect was enhanced by SA. TMV normally kills N. benthamiana plants but although MtRDR1-transgenic plants initially displayed virus-induced necrosis they subsequently recovered. Recovery from disease was markedly enhanced by SA treatment in MtRDR1-transgenic plants whereas in control plants SA delayed but did not prevent systemic necrosis and death. Following SA treatment of MtRDR1-transgenic plants, extractable RDR enzyme activity was increased and Western blot analysis of RDR extracts revealed a band cross-reacting with an antibody raised against MtRDR1. Expression of MtRDR1 in the transgenic N. benthamiana plants was driven by a constitutive 35S promoter derived from cauliflower mosaic virus, confirmed to be non-responsive to SA. This suggests that the effects of SA on MtRDR1 are exerted at a post-transcriptional level. CONCLUSIONS MtRDR1 inhibits severe symptom development by limiting spread of virus into the growing tips of infected plants. Thus, RDR1 may act in a similar fashion to RDR6. MtRDR1 and SA acted additively to further promote recovery from disease symptoms in MtRDR1-transgenic plants. Thus it is possible that SA promotes MtRDR1 activity and/or stability through post-transcriptional effects.
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Affiliation(s)
- Wing-Sham Lee
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK.
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.
| | - Shih-Feng Fu
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK.
- Department of Biology, National Changhua University of Education, 1 Jin-De Road, Changhua City, 500, Taiwan.
| | - Zheng Li
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK.
| | - Alex M Murphy
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK.
| | - Elizabeth A Dobson
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK.
| | - Laura Garland
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK.
| | - Srinivasa Rao Chaluvadi
- Plant Biology Division, Samuel Roberts Noble Foundation, Inc, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA.
| | - Mathew G Lewsey
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK.
- Centre for AgriBioscience, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Australia.
| | - Richard S Nelson
- Plant Biology Division, Samuel Roberts Noble Foundation, Inc, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA.
| | - John P Carr
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK.
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Weirauch MT, Yang A, Albu M, Cote AG, Montenegro-Montero A, Drewe P, Najafabadi HS, Lambert SA, Mann I, Cook K, Zheng H, Goity A, van Bakel H, Lozano JC, Galli M, Lewsey MG, Huang E, Mukherjee T, Chen X, Reece-Hoyes JS, Govindarajan S, Shaulsky G, Walhout AJM, Bouget FY, Ratsch G, Larrondo LF, Ecker JR, Hughes TR. Determination and inference of eukaryotic transcription factor sequence specificity. Cell 2014; 158:1431-1443. [PMID: 25215497 DOI: 10.1016/j.cell.2014.08.009] [Citation(s) in RCA: 1084] [Impact Index Per Article: 108.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 04/03/2014] [Accepted: 08/06/2014] [Indexed: 10/24/2022]
Abstract
Transcription factor (TF) DNA sequence preferences direct their regulatory activity, but are currently known for only ∼1% of eukaryotic TFs. Broadly sampling DNA-binding domain (DBD) types from multiple eukaryotic clades, we determined DNA sequence preferences for >1,000 TFs encompassing 54 different DBD classes from 131 diverse eukaryotes. We find that closely related DBDs almost always have very similar DNA sequence preferences, enabling inference of motifs for ∼34% of the ∼170,000 known or predicted eukaryotic TFs. Sequences matching both measured and inferred motifs are enriched in chromatin immunoprecipitation sequencing (ChIP-seq) peaks and upstream of transcription start sites in diverse eukaryotic lineages. SNPs defining expression quantitative trait loci in Arabidopsis promoters are also enriched for predicted TF binding sites. Importantly, our motif "library" can be used to identify specific TFs whose binding may be altered by human disease risk alleles. These data present a powerful resource for mapping transcriptional networks across eukaryotes.
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Affiliation(s)
- Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology (CAGE) and Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Banting and Best Department of Medical Research and Donnelly Centre, University of Toronto, Toronto ON M5S 3E1, Canada
| | - Ally Yang
- Banting and Best Department of Medical Research and Donnelly Centre, University of Toronto, Toronto ON M5S 3E1, Canada
| | - Mihai Albu
- Banting and Best Department of Medical Research and Donnelly Centre, University of Toronto, Toronto ON M5S 3E1, Canada
| | - Atina G Cote
- Banting and Best Department of Medical Research and Donnelly Centre, University of Toronto, Toronto ON M5S 3E1, Canada
| | - Alejandro Montenegro-Montero
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Philipp Drewe
- Computational Biology Center, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Hamed S Najafabadi
- Banting and Best Department of Medical Research and Donnelly Centre, University of Toronto, Toronto ON M5S 3E1, Canada
| | - Samuel A Lambert
- Department of Molecular Genetics, University of Toronto, Toronto ON M5S 1A8, Canada
| | - Ishminder Mann
- Banting and Best Department of Medical Research and Donnelly Centre, University of Toronto, Toronto ON M5S 3E1, Canada
| | - Kate Cook
- Department of Molecular Genetics, University of Toronto, Toronto ON M5S 1A8, Canada
| | - Hong Zheng
- Banting and Best Department of Medical Research and Donnelly Centre, University of Toronto, Toronto ON M5S 3E1, Canada
| | - Alejandra Goity
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Harm van Bakel
- Banting and Best Department of Medical Research and Donnelly Centre, University of Toronto, Toronto ON M5S 3E1, Canada; Icahn Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Jean-Claude Lozano
- Sorbonne Universités, UPMC Univ Paris 06, CNRS UMR 7621, CNRS, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66650 Banyuls/mer, France
| | - Mary Galli
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Mathew G Lewsey
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Eryong Huang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tuhin Mukherjee
- Department of Electronic and Computing Systems, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Xiaoting Chen
- Department of Electronic and Computing Systems, University of Cincinnati, Cincinnati, OH 45221, USA
| | - John S Reece-Hoyes
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | | | - Gad Shaulsky
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Albertha J M Walhout
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - François-Yves Bouget
- Sorbonne Universités, UPMC Univ Paris 06, CNRS UMR 7621, CNRS, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66650 Banyuls/mer, France
| | - Gunnar Ratsch
- Computational Biology Center, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Luis F Larrondo
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Joseph R Ecker
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Timothy R Hughes
- Banting and Best Department of Medical Research and Donnelly Centre, University of Toronto, Toronto ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto ON M5S 1A8, Canada.
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Zhou T, Murphy AM, Lewsey MG, Westwood JH, Zhang HM, González I, Canto T, Carr JP. Domains of the cucumber mosaic virus 2b silencing suppressor protein affecting inhibition of salicylic acid-induced resistance and priming of salicylic acid accumulation during infection. J Gen Virol 2014; 95:1408-1413. [PMID: 24633701 PMCID: PMC4027040 DOI: 10.1099/vir.0.063461-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Accepted: 03/13/2014] [Indexed: 11/18/2022] Open
Abstract
The cucumber mosaic virus (CMV) 2b silencing suppressor protein allows the virus to overcome resistance to replication and local movement in inoculated leaves of plants treated with salicylic acid (SA), a resistance-inducing plant hormone. In Arabidopsis thaliana plants systemically infected with CMV, the 2b protein also primes the induction of SA biosynthesis during this compatible interaction. We found that CMV infection of susceptible tobacco (Nicotiana tabacum) also induced SA accumulation. Utilization of mutant 2b proteins expressed during infection of tobacco showed that the N- and C-terminal domains, which had previously been implicated in regulation of symptom induction, were both required for subversion of SA-induced resistance, while all mutants tested except those affecting the putative phosphorylation domain had lost the ability to prime SA accumulation and expression of the SA-induced marker gene PR-1.
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Affiliation(s)
- Tao Zhou
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
- Department of Plant Pathology, China Agricultural University, 2 Yuanmingyuan West Rd, Beijing 100193, PR China
| | - Alex M. Murphy
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Mathew G. Lewsey
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Jack H. Westwood
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Heng-Mu Zhang
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, 198 Shiqiao Rd, Hangzhou 310021, Zhejiang, PR China
| | - Inmaculada González
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
- Centro de Investigaciones Biológicas, CIB, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Tomás Canto
- Centro de Investigaciones Biológicas, CIB, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - John P. Carr
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
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Westwood JH, Lewsey MG, Murphy AM, Tungadi T, Bates A, Gilligan CA, Carr JP. Interference with jasmonic acid-regulated gene expression is a general property of viral suppressors of RNA silencing but only partly explains virus-induced changes in plant-aphid interactions. J Gen Virol 2014; 95:733-739. [PMID: 24362960 PMCID: PMC3929171 DOI: 10.1099/vir.0.060624-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 12/16/2013] [Indexed: 11/18/2022] Open
Abstract
The cucumber mosaic virus (CMV) 2b viral suppressor of RNA silencing (VSR) inhibits host responses to jasmonic acid (JA), a chemical signal regulating resistance to insects. Previous experiments with a CMV subgroup IA strain and its 2b gene deletion mutant suggested that VSRs might neutralize aphid (Myzus persicae) resistance by inhibiting JA-regulated gene expression. To further investigate this, we examined JA-regulated gene expression and aphid performance in Nicotiana benthamiana infected with Potato virus X, Potato virus Y, Tobacco mosaic virus and a subgroup II CMV strain, as well as in transgenic plants expressing corresponding VSRs (p25, HC-Pro, 126 kDa and 2b). All the viruses or their VSRs inhibited JA-induced gene expression. However, this did not always correlate with enhanced aphid performance. Thus, VSRs are not the sole viral determinants of virus-induced changes in host-aphid interactions and interference with JA-regulated gene expression cannot completely explain enhanced aphid performance on virus-infected plants.
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Affiliation(s)
- Jack H Westwood
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
| | - Mathew G Lewsey
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
| | - Alex M Murphy
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
| | - Trisna Tungadi
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
| | - Anne Bates
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
| | - Christopher A Gilligan
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
| | - John P Carr
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
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Westwood JH, Groen SC, Du Z, Murphy AM, Anggoro DT, Tungadi T, Luang-In V, Lewsey MG, Rossiter JT, Powell G, Smith AG, Carr JP. A trio of viral proteins tunes aphid-plant interactions in Arabidopsis thaliana. PLoS One 2013; 8:e83066. [PMID: 24349433 PMCID: PMC3859657 DOI: 10.1371/journal.pone.0083066] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 11/07/2013] [Indexed: 12/23/2022] Open
Abstract
Background Virus-induced deterrence to aphid feeding is believed to promote plant virus transmission by encouraging migration of virus-bearing insects away from infected plants. We investigated the effects of infection by an aphid-transmitted virus, cucumber mosaic virus (CMV), on the interaction of Arabidopsis thaliana, one of the natural hosts for CMV, with Myzus persicae (common names: ‘peach-potato aphid’, ‘green peach aphid’). Methodology/Principal Findings Infection of Arabidopsis (ecotype Col-0) with CMV strain Fny (Fny-CMV) induced biosynthesis of the aphid feeding-deterrent 4-methoxy-indol-3-yl-methylglucosinolate (4MI3M). 4MI3M inhibited phloem ingestion by aphids and consequently discouraged aphid settling. The CMV 2b protein is a suppressor of antiviral RNA silencing, which has previously been implicated in altering plant-aphid interactions. Its presence in infected hosts enhances the accumulation of CMV and the other four viral proteins. Another viral gene product, the 2a protein (an RNA-dependent RNA polymerase), triggers defensive signaling, leading to increased 4MI3M accumulation. The 2b protein can inhibit ARGONAUTE1 (AGO1), a host factor that both positively-regulates 4MI3M biosynthesis and negatively-regulates accumulation of substance(s) toxic to aphids. However, the 1a replicase protein moderated 2b-mediated inhibition of AGO1, ensuring that aphids were deterred from feeding but not poisoned. The LS strain of CMV did not induce feeding deterrence in Arabidopsis ecotype Col-0. Conclusions/Significance Inhibition of AGO1 by the 2b protein could act as a booby trap since this will trigger antibiosis against aphids. However, for Fny-CMV the interplay of three viral proteins (1a, 2a and 2b) appears to balance the need of the virus to inhibit antiviral silencing, while inducing a mild resistance (antixenosis) that is thought to promote transmission. The strain-specific effects of CMV on Arabidopsis-aphid interactions, and differences between the effects of Fny-CMV on this plant and those seen previously in tobacco (inhibition of resistance to aphids) may have important epidemiological consequences.
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Affiliation(s)
- Jack H Westwood
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Simon C Groen
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Zhiyou Du
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Alex M Murphy
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Damar Tri Anggoro
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Trisna Tungadi
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | | | - Mathew G Lewsey
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | | | | | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - John P Carr
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
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Schweizer F, Fernández-Calvo P, Zander M, Diez-Diaz M, Fonseca S, Glauser G, Lewsey MG, Ecker JR, Solano R, Reymond P. Arabidopsis basic helix-loop-helix transcription factors MYC2, MYC3, and MYC4 regulate glucosinolate biosynthesis, insect performance, and feeding behavior. Plant Cell 2013; 25:3117-32. [PMID: 23943862 PMCID: PMC3784603 DOI: 10.1105/tpc.113.115139] [Citation(s) in RCA: 327] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 07/18/2013] [Accepted: 07/26/2013] [Indexed: 05/17/2023]
Abstract
Arabidopsis thaliana plants fend off insect attack by constitutive and inducible production of toxic metabolites, such as glucosinolates (GSs). A triple mutant lacking MYC2, MYC3, and MYC4, three basic helix-loop-helix transcription factors that are known to additively control jasmonate-related defense responses, was shown to have a highly reduced expression of GS biosynthesis genes. The myc2 myc3 myc4 (myc234) triple mutant was almost completely devoid of GS and was extremely susceptible to the generalist herbivore Spodoptera littoralis. On the contrary, the specialist Pieris brassicae was unaffected by the presence of GS and preferred to feed on wild-type plants. In addition, lack of GS in myc234 drastically modified S. littoralis feeding behavior. Surprisingly, the expression of MYB factors known to regulate GS biosynthesis genes was not altered in myc234, suggesting that MYC2/MYC3/MYC4 are necessary for direct transcriptional activation of GS biosynthesis genes. To support this, chromatin immunoprecipitation analysis showed that MYC2 binds directly to the promoter of several GS biosynthesis genes in vivo. Furthermore, yeast two-hybrid and pull-down experiments indicated that MYC2/MYC3/MYC4 interact directly with GS-related MYBs. This specific MYC-MYB interaction plays a crucial role in the regulation of defense secondary metabolite production and underlines the importance of GS in shaping plant interactions with adapted and nonadapted herbivores.
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Affiliation(s)
- Fabian Schweizer
- Department of Plant Molecular Biology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Patricia Fernández-Calvo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología–Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Mark Zander
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Monica Diez-Diaz
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología–Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Sandra Fonseca
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología–Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Gaétan Glauser
- Chemical Analytical Service of the Swiss Plant Science Web, University of Neuchâtel, 2009 Neuchatel, Switzerland
| | - Mathew G. Lewsey
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Joseph R. Ecker
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Roberto Solano
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología–Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, 28049 Madrid, Spain
| | - Philippe Reymond
- Department of Plant Molecular Biology, University of Lausanne, CH-1015 Lausanne, Switzerland
- Address correspondence to
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38
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Ziebell H, Murphy AM, Groen SC, Tungadi T, Westwood JH, Lewsey MG, Moulin M, Kleczkowski A, Smith AG, Stevens M, Powell G, Carr JP. Cucumber mosaic virus and its 2b RNA silencing suppressor modify plant-aphid interactions in tobacco. Sci Rep 2011; 1:187. [PMID: 22355702 PMCID: PMC3240964 DOI: 10.1038/srep00187] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 11/11/2011] [Indexed: 11/22/2022] Open
Abstract
The cucumber mosaic virus (CMV) 2b protein not only inhibits anti-viral RNA silencing but also quenches transcriptional responses of plant genes to jasmonic acid, a key signalling molecule in defence against insects. This suggested that it might affect interactions between infected plants and aphids, insects that transmit CMV. We found that infection of tobacco with a 2b gene deletion mutant (CMVΔ2b) induced strong resistance to aphids (Myzus persicae) while CMV infection fostered aphid survival. Using electrical penetration graph methodology we found that higher proportions of aphids showed sustained phloem ingestion on CMV-infected plants than on CMVΔ2b-infected or mock-inoculated plants although this did not increase the rate of growth of individual aphids. This indicates that while CMV infection or certain viral gene products might elicit aphid resistance, the 2b protein normally counteracts this during a wild-type CMV infection. Our findings suggest that the 2b protein could indirectly affect aphid-mediated virus transmission.
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Affiliation(s)
- Heiko Ziebell
- University of Cambridge, Department of Plant Sciences, Downing Street, Cambridge, CB2 3EA, UK
- Present address: Julius Kühn Institut, Federal Research Centre for Cultivated Plants, Institute of Epidemiology and Pathogen Diagnostics, Messeweg 11–12, 38104 Braunschweig, Germany
- These authors contributed equally to the work
| | - Alex M. Murphy
- University of Cambridge, Department of Plant Sciences, Downing Street, Cambridge, CB2 3EA, UK
- These authors contributed equally to the work
| | - Simon C. Groen
- University of Cambridge, Department of Plant Sciences, Downing Street, Cambridge, CB2 3EA, UK
| | - Trisna Tungadi
- University of Cambridge, Department of Plant Sciences, Downing Street, Cambridge, CB2 3EA, UK
| | - Jack H. Westwood
- University of Cambridge, Department of Plant Sciences, Downing Street, Cambridge, CB2 3EA, UK
| | - Mathew G. Lewsey
- University of Cambridge, Department of Plant Sciences, Downing Street, Cambridge, CB2 3EA, UK
- Present address: The Salk Institute for Biological Studies, Plant Biology Laboratory, 10010 North Torrey Pines Road, La Jolla, CA 92037 USA
| | - Michael Moulin
- University of Cambridge, Department of Plant Sciences, Downing Street, Cambridge, CB2 3EA, UK
- Present address: Plant Biochemistry & Physiology, BIVEG, University of Geneva-Science III, 30 Quai Ernest Ansermet, 1211 Geneva 4, Switzerland
| | - Adam Kleczkowski
- University of Stirling, Computing Sciences and Mathematics, School of Natural Sciences, Stirling FK9 4LA, UK
| | - Alison G. Smith
- University of Cambridge, Department of Plant Sciences, Downing Street, Cambridge, CB2 3EA, UK
| | - Mark Stevens
- Broom's Barn Research Station, Higham, Bury St Edmunds, IP28 6NP, UK
| | - Glen Powell
- Imperial College London, Department of Plant and Microbial Sciences, Exhibition Road, London SW7 2AZ, UK
| | - John P. Carr
- University of Cambridge, Department of Plant Sciences, Downing Street, Cambridge, CB2 3EA, UK
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Schmitz RJ, Schultz MD, Lewsey MG, O'Malley RC, Urich MA, Libiger O, Schork NJ, Ecker JR. Transgenerational epigenetic instability is a source of novel methylation variants. Science 2011; 334:369-73. [PMID: 21921155 DOI: 10.1126/science.1212959] [Citation(s) in RCA: 453] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Epigenetic information, which may affect an organism's phenotype, can be stored and stably inherited in the form of cytosine DNA methylation. Changes in DNA methylation can produce meiotically stable epialleles that affect transcription and morphology, but the rates of spontaneous gain or loss of DNA methylation are unknown. We examined spontaneously occurring variation in DNA methylation in Arabidopsis thaliana plants propagated by single-seed descent for 30 generations. We identified 114,287 CG single methylation polymorphisms and 2485 CG differentially methylated regions (DMRs), both of which show patterns of divergence compared with the ancestral state. Thus, transgenerational epigenetic variation in DNA methylation may generate new allelic states that alter transcription, providing a mechanism for phenotypic diversity in the absence of genetic mutation.
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Affiliation(s)
- Robert J Schmitz
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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40
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Abstract
BACKGROUND Argonaute (AGO) proteins bind to small-interfering (si)RNAs and micro (mi)RNAs to target RNA silencing against viruses, transgenes and in regulation of mRNAs. Plants encode multiple AGO proteins but, in Arabidopsis, only AGO1 is known to have an antiviral role. METHODOLOGY/PRINCIPAL FINDINGS To uncover the roles of specific AGOs in limiting virus accumulation we inoculated turnip crinkle virus (TCV) to Arabidopsis plants that were mutant for each of the ten AGO genes. The viral symptoms on most of the plants were the same as on wild type plants although the ago2 mutants were markedly hyper-susceptible to this virus. ago2 plants were also hyper-susceptible to cucumber mosaic virus (CMV), confirming that the antiviral role of AGO2 is not specific to a single virus. For both viruses, this phenotype was associated with transient increase in virus accumulation. In wild type plants the AGO2 protein was induced by TCV and CMV infection. CONCLUSIONS/SIGNIFICANCE Based on these results we propose that there are multiple layers to RNA-mediated defense and counter-defense in the interactions between plants and their viruses. AGO1 represents a first layer. With some viruses, including TCV and CMV, this layer is overcome by viral suppressors of silencing that can target AGO1 and a second layer involving AGO2 limits virus accumulation. The second layer is activated when the first layer is suppressed because AGO2 is repressed by AGO1 via miR403. The activation of the second layer is therefore a direct consequence of the loss of the first layer of defense.
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Affiliation(s)
- Jagger J. W. Harvey
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Mathew G. Lewsey
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Kanu Patel
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Jack Westwood
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Susanne Heimstädt
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - John P. Carr
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - David C. Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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41
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Lewsey MG, Murphy AM, Maclean D, Dalchau N, Westwood JH, Macaulay K, Bennett MH, Moulin M, Hanke DE, Powell G, Smith AG, Carr JP. Disruption of two defensive signaling pathways by a viral RNA silencing suppressor. Mol Plant Microbe Interact 2010; 23:835-45. [PMID: 20521947 DOI: 10.1094/mpmi-23-7-0835] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The Cucumber mosaic virus (CMV) 2b counter-defense protein disrupts plant antiviral mechanisms mediated by RNA silencing and salicylic acid (SA). We used microarrays to investigate defensive gene expression in 2b-transgenic Arabidopsis thaliana plants. Surprisingly, 2b inhibited expression of few SA-regulated genes and, in some instances, enhanced the effect of SA on certain genes. Strikingly, the 2b protein inhibited changes in the expression of 90% of genes regulated by jasmonic acid (JA). Consistent with this, infection of plants with CMV, but not the 2b gene-deletion mutant CMVDelta2b, strongly inhibited JA-inducible gene expression. JA levels were unaffected by infection with either CMV or CMVDelta2b. Although the CMV-Arabidopsis interaction is a compatible one, SA accumulation, usually considered to be an indicator of plant resistance, was increased in CMV-infected plants but not in CMVDelta2b-infected plants. Thus, the 2b protein inhibits JA signaling at a step downstream of JA biosynthesis but it primes induction of SA biosynthesis by another CMV gene product or by the process of infection itself. Like many plant viruses, CMV is aphid transmitted. JA is important in plant defense against insects. This raises the possibility that disruption of JA-mediated gene expression by the 2b protein may influence CMV transmission by aphids.
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42
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Abstract
Earlier this year plant scientists met in Santa Fe, New Mexico at the Keystone Symposium "RNA Silencing Mechanisms in Plants". Sessions included small RNA biogenesis and signalling, development and stress responses, small RNA-directed DNA methylation, and interaction with pathogens. This report highlights some of the prominent and recurring themes at the meeting and emerging arenas of future research.
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Affiliation(s)
- Rebecca A Mosher
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.
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Lewsey MG, González I, Kalinina NO, Palukaitis P, Canto T, Carr JP. Symptom induction and RNA silencing suppression by the cucumber mosaic virus 2b protein. Plant Signal Behav 2010; 5:705-8. [PMID: 20404501 PMCID: PMC3001565 DOI: 10.4161/psb.5.6.11643] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The 2b protein encoded by Cucumber mosaic virus (CMV) and other cucumoviruses is multifunctional, having roles in local and systemic virus movement, symptom determination, evasion of defense mediated by salicylic acid, and in suppression of antiviral RNA silencing. It also perturbs silencing-mediated regulation of host transcripts, suggesting that another function of 2b protein is to manipulate host gene expression and physiology in a way that may aid the virus. The 2b proteins encoded by the various cucumoviruses (CMV strains, as well as Tomato aspermy virus and Peanut stunt virus) share conserved amino acid sequence domains, suggesting that these might determine specific functions of the protein. We analyzed the effect of mutations in these domains on functions of the 2b protein during viral infection. This revealed that binding of short RNAs, the key determinants of RNA silencing specificity, correlates with RNA silencing suppression activity. Two putative phosphorylation sites were found to be required for virus symptom induction, despite having no influence on RNA silencing suppression. This indicates that the ability to suppress silencing is not the only factor affecting symptom induction by the 2b protein. In accordance with this, our studies also revealed that the 2b protein acts synergistically with some other CMV product(s) to induce symptoms, and that the role of the 2b protein in symptom determination is host species specific.
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Affiliation(s)
- Mathew G Lewsey
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
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González I, Martínez L, Rakitina DV, Lewsey MG, Atencio FA, Llave C, Kalinina NO, Carr JP, Palukaitis P, Canto T. Cucumber mosaic virus 2b protein subcellular targets and interactions: their significance to RNA silencing suppressor activity. Mol Plant Microbe Interact 2010; 23:294-303. [PMID: 20121451 DOI: 10.1094/mpmi-23-3-0294] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The RNA silencing suppressor activity of the 2b protein of Cucumber mosaic virus (CMV) has been variously attributed to its nuclear targeting, its interaction with and inhibition of Argonaute 1 (AGO1), or its ability to bind small RNAs in vitro. In addition, the 2b ortholog of Tomato aspermy virus forms aggregates and binds RNAs in vitro. We have further studied the relationships between CMV 2b protein silencing suppressor activity and its subcellular distribution, protein-protein interactions in vivo, and interactions with small interfering RNAs in vitro. To do this, we tagged the protein with fluorescent markers and showed that it retained suppressor activity. We showed that the 2b protein is present in the nucleolus and that it self-interacts and interacts with AGO1 and AGO4 in vivo. Using a battery of mutants, we showed that the putative nuclear localization signals and phosphorylation motif of the 2b protein are not required for self-interaction or for interaction with AGO proteins. The occurrence of neither of these interactions or of nucleolar targeting was sufficient to provide local silencing-suppression activity. In contrast, the ability of the 2b protein to bind small RNAs appears to be indispensable for silencing suppressor function.
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Affiliation(s)
- Inmaculada González
- Centro de Investigaciones Biológicas, CIB, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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Lewsey MG, Carr JP. Effects of DICER-like proteins 2, 3 and 4 on cucumber mosaic virus and tobacco mosaic virus infections in salicylic acid-treated plants. J Gen Virol 2009; 90:3010-3014. [DOI: 10.1099/vir.0.014555-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Salicylic acid (SA)-mediated resistance and RNA silencing are both important plant antiviral defence mechanisms. To investigate overlap between these resistance phenomena, we examined the ability of mutant Arabidopsis thaliana plants lacking DICER-like (DCL) endoribonucleases 2, 3 and 4 to exhibit SA-induced defence. We found that in dcl2/3/4 triple mutant plants, treatment with exogenous SA stimulated resistance to two positive-sense RNA viruses: cucumber mosaic virus and tobacco mosaic virus. We conclude that DCLs 2, 3 and 4, which are the predominant DCL endoribonucleases involved in silencing of positive-sense RNA viruses, are not required for effective SA-induced resistance to these viruses. However, the findings do not exclude RNA silencing from making a contribution to SA-mediated resistance in wild-type plants.
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Affiliation(s)
- Mathew G. Lewsey
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - John P. Carr
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
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