1
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Wu HYL, Ai Q, Teixeira RT, Nguyen PHT, Song G, Montes C, Elmore JM, Walley JW, Hsu PY. Improved super-resolution ribosome profiling reveals prevalent translation of upstream ORFs and small ORFs in Arabidopsis. Plant Cell 2024; 36:510-539. [PMID: 38000896 PMCID: PMC10896292 DOI: 10.1093/plcell/koad290] [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: 08/13/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 11/26/2023]
Abstract
A crucial step in functional genomics is identifying actively translated ORFs and linking them to biological functions. The challenge lies in identifying short ORFs, as their identification is greatly influenced by data quality and depth. Here, we improved the coverage of super-resolution Ribo-seq in Arabidopsis (Arabidopsis thaliana), revealing uncharacterized translation events for nuclear, chloroplastic, and mitochondrial genes. Assisted by a transcriptome assembly, we identified 7,751 unconventional translation events, comprising 6,996 upstream ORFs (uORFs) and 209 downstream ORFs on annotated protein-coding genes, as well as 546 ORFs in presumed noncoding RNAs. Proteomic data confirmed the production of stable proteins from some of these unannotated translation events. We present evidence of active translation from primary transcripts of trans-acting small interfering RNAs (TAS1-4) and microRNAs (pri-MIR163 and pri-MIR169) and periodic ribosome stalling supporting cotranslational decay. Additionally, we developed a method for identifying extremely short uORFs, including 370 minimum uORFs (AUG-stop), and 2,921 tiny uORFs (2 to 10 amino acids) and 681 uORFs that overlap with each other. Remarkably, these short uORFs exhibit strong translational repression as do longer uORFs. We also systematically discovered 594 uORFs regulated by alternative splicing, suggesting widespread isoform-specific translational control. Finally, these prevalent uORFs are associated with numerous important pathways. In summary, our improved Arabidopsis translational landscape provides valuable resources to study gene expression regulation.
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Affiliation(s)
- Hsin-Yen Larry Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Qiaoyun Ai
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Rita Teresa Teixeira
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Phong H T Nguyen
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Gaoyuan Song
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Christian Montes
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - J Mitch Elmore
- 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
| | - Polly Yingshan Hsu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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2
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Malik S, Walley JW. Unveiling a new regulator: Vacuolar V-ATPase mediates brassinosteroid signaling in Arabidopsis. Mol Plant 2024; 17:227-229. [PMID: 38155571 DOI: 10.1016/j.molp.2023.12.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/24/2023] [Accepted: 12/26/2023] [Indexed: 12/30/2023]
Affiliation(s)
- Shikha Malik
- 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.
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3
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Watkins JM, Montes C, Clark NM, Song G, Oliveira CC, Mishra B, Brachova L, Seifert CM, Mitchell MS, Yang J, Braga Dos Reis PA, Urano D, Muktar MS, Walley JW, Jones AM. Phosphorylation Dynamics in a flg22-Induced, G Protein-Dependent Network Reveals the AtRGS1 Phosphatase. Mol Cell Proteomics 2024; 23:100705. [PMID: 38135118 PMCID: PMC10837098 DOI: 10.1016/j.mcpro.2023.100705] [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] [Received: 04/03/2023] [Revised: 11/22/2023] [Accepted: 12/19/2023] [Indexed: 12/24/2023] Open
Abstract
The microbe-associated molecular pattern flg22 is recognized in a flagellin-sensitive 2-dependent manner in root tip cells. Here, we show a rapid and massive change in protein abundance and phosphorylation state of the Arabidopsis root cell proteome in WT and a mutant deficient in heterotrimeric G-protein-coupled signaling. flg22-induced changes fall on proteins comprising a subset of this proteome, the heterotrimeric G protein interactome, and on highly-populated hubs of the immunity network. Approximately 95% of the phosphorylation changes in the heterotrimeric G-protein interactome depend, at least partially, on a functional G protein complex. One member of this interactome is ATBα, a substrate-recognition subunit of a protein phosphatase 2A complex and an interactor to Arabidopsis thaliana Regulator of G Signaling 1 protein (AtRGS1), a flg22-phosphorylated, 7-transmembrane spanning modulator of the nucleotide-binding state of the core G-protein complex. A null mutation of ATBα strongly increases basal endocytosis of AtRGS1. AtRGS1 steady-state protein level is lower in the atbα mutant in a proteasome-dependent manner. We propose that phosphorylation-dependent endocytosis of AtRGS1 is part of the mechanism to degrade AtRGS1, thus sustaining activation of the heterotrimeric G protein complex required for the regulation of system dynamics in innate immunity. The PP2A(ATBα) complex is a critical regulator of this signaling pathway.
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Affiliation(s)
- Justin M Watkins
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Christian Montes
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Natalie M Clark
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Celio Cabral Oliveira
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Biochemistry and Molecular Biology/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Bharat Mishra
- Department of Biology, University of Alabama-Birmingham, Birmingham, Alabama, USA
| | - Libuse Brachova
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Clara M Seifert
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Malek S Mitchell
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jing Yang
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Daisuke Urano
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - M Shahid Muktar
- Department of Biology, University of Alabama-Birmingham, Birmingham, Alabama, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA.
| | - Alan M Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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4
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Liao CY, Pu Y, Nolan TM, Montes C, Guo H, Walley JW, Yin Y, Bassham DC. Brassinosteroids modulate autophagy through phosphorylation of RAPTOR1B by the GSK3-like kinase BIN2 in Arabidopsis. Autophagy 2023; 19:1293-1310. [PMID: 36151786 PMCID: PMC10012961 DOI: 10.1080/15548627.2022.2124501] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Macroautophagy/autophagy is a conserved recycling process that maintains cellular homeostasis during environmental stress. Autophagy is negatively regulated by TOR (target of rapamycin), a nutrient-regulated protein kinase that in plants is activated by several phytohormones, leading to increased growth. However, the detailed molecular mechanisms by which TOR integrates autophagy and hormone signaling are poorly understood. Here, we show that TOR modulates brassinosteroid (BR)-regulated plant growth and stress-response pathways. Active TOR was required for full BR-mediated growth in Arabidopsis thaliana. Autophagy was constitutively up-regulated upon blocking BR biosynthesis or signaling, and down-regulated by increasing the activity of the BR pathway. BIN2 (brassinosteroid-insensitive 2) kinase, a GSK3-like kinase functioning as a negative regulator in BR signaling, directly phosphorylated RAPTOR1B (regulatory-associated protein of TOR 1B), a substrate-recruiting subunit in the TOR complex, at a conserved serine residue within a typical BIN2 phosphorylation motif. Mutation of RAPTOR1B serine 916 to alanine, to block phosphorylation by BIN2, repressed autophagy and increased phosphorylation of the TOR substrate ATG13a (autophagy-related protein 13a). By contrast, this mutation had only a limited effect on growth. We present a model in which RAPTOR1B is phosphorylated and inhibited by BIN2 when BRs are absent, activating the autophagy pathway. When BRs signal and inhibit BIN2, RAPTOR1B is thus less inhibited by BIN2 phosphorylation. This leads to increased TOR activity and ATG13a phosphorylation, and decreased autophagy activity. Our studies define a new mechanism by which coordination between BR and TOR signaling pathways helps to maintain the balance between plant growth and stress responses.
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Affiliation(s)
- Ching-Yi Liao
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Yunting Pu
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Trevor M Nolan
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Christian Montes
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Hongqing Guo
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Yanhai Yin
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Diane C Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
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5
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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] [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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6
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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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7
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Montes C, Wang P, Liao C, Nolan TM, Song G, Clark NM, Elmore JM, Guo H, Bassham DC, Yin Y, Walley JW. Integration of multi-omics data reveals interplay between brassinosteroid and Target of Rapamycin Complex signaling in Arabidopsis. New Phytol 2022; 236:893-910. [PMID: 35892179 PMCID: PMC9804314 DOI: 10.1111/nph.18404] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 04/06/2022] [Accepted: 07/16/2022] [Indexed: 06/01/2023]
Abstract
Brassinosteroids (BRs) and Target of Rapamycin Complex (TORC) are two major actors coordinating plant growth and stress responses. Brassinosteroids function through a signaling pathway to extensively regulate gene expression and TORC is known to regulate translation and autophagy. Recent studies have revealed connections between these two pathways, but a system-wide view of their interplay is still missing. We quantified the level of 23 975 transcripts, 11 183 proteins, and 27 887 phosphorylation sites in wild-type Arabidopsis thaliana and in mutants with altered levels of either BRASSINOSTEROID INSENSITIVE 2 (BIN2) or REGULATORY ASSOCIATED PROTEIN OF TOR 1B (RAPTOR1B), two key players in BR and TORC signaling, respectively. We found that perturbation of BIN2 or RAPTOR1B levels affects a common set of gene-products involved in growth and stress responses. Furthermore, we used the multi-omic data to reconstruct an integrated signaling network. We screened 41 candidate genes identified from the reconstructed network and found that loss of function mutants of many of these proteins led to an altered BR response and/or modulated autophagy activity. Altogether, these results establish a predictive network that defines different layers of molecular interactions between BR- or TORC-regulated growth and autophagy.
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Affiliation(s)
- Christian Montes
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIA50011USA
| | - Ping Wang
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIA50011USA
| | - Ching‐Yi Liao
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIA50011USA
| | - Trevor M. Nolan
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIA50011USA
- Department of BiologyDuke UniversityDurhamNC27708USA
| | - Gaoyuan Song
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIA50011USA
| | - Natalie M. Clark
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIA50011USA
| | - J. Mitch Elmore
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIA50011USA
- USDA‐ARS Cereal Disease LaboratoryUniversity of MinnesotaSt PaulMN55108USA
| | - Hongqing Guo
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIA50011USA
| | - Diane C. Bassham
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIA50011USA
| | - Yanhai Yin
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIA50011USA
- Plant Sciences InstituteIowa State UniversityAmesIA50011USA
| | - Justin W. Walley
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIA50011USA
- Plant Sciences InstituteIowa State UniversityAmesIA50011USA
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8
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Wang P, Clark NM, Nolan TM, Song G, Bartz PM, Liao CY, Montes-Serey C, Katz E, Polko JK, Kieber JJ, Kliebenstein DJ, Bassham DC, Walley JW, Yin Y, Guo H. Integrated omics reveal novel functions and underlying mechanisms of the receptor kinase FERONIA in Arabidopsis thaliana. Plant Cell 2022; 34:2594-2614. [PMID: 35435236 PMCID: PMC9252503 DOI: 10.1093/plcell/koac111] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 04/09/2022] [Indexed: 05/20/2023]
Abstract
The receptor kinase FERONIA (FER) is a versatile regulator of plant growth and development, biotic and abiotic stress responses, and reproduction. To gain new insights into the molecular interplay of these processes and to identify new FER functions, we carried out quantitative transcriptome, proteome, and phosphoproteome profiling of Arabidopsis (Arabidopsis thaliana) wild-type and fer-4 loss-of-function mutant plants. Gene ontology terms for phytohormone signaling, abiotic stress, and biotic stress were significantly enriched among differentially expressed transcripts, differentially abundant proteins, and/or misphosphorylated proteins, in agreement with the known roles for FER in these processes. Analysis of multiomics data and subsequent experimental evidence revealed previously unknown functions for FER in endoplasmic reticulum (ER) body formation and glucosinolate biosynthesis. FER functions through the transcription factor NAI1 to mediate ER body formation. FER also negatively regulates indole glucosinolate biosynthesis, partially through NAI1. Furthermore, we found that a group of abscisic acid (ABA)-induced transcription factors is hypophosphorylated in the fer-4 mutant and demonstrated that FER acts through the transcription factor ABA INSENSITIVE5 (ABI5) to negatively regulate the ABA response during cotyledon greening. Our integrated omics study, therefore, reveals novel functions for FER and provides new insights into the underlying mechanisms of FER function.
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Affiliation(s)
- Ping Wang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Natalie M Clark
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | | | - Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | - Parker M Bartz
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Ching-Yi Liao
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Christian Montes-Serey
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | - Ella Katz
- Department of Plant Science, University of California, Davis, California 95616, USA
| | - Joanna K Polko
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Joseph J Kieber
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | | | - Diane C Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
- Plant Sciences Institutes, Iowa State University, Ames, Iowa 50011, USA
| | - Yanhai Yin
- Author for correspondence: (H.G.); (Y.Y)
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9
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Chapman AVE, Elmore JM, McReynolds M, Walley JW, Wise RP. SGT1-Specific Domain Mutations Impair Interactions with the Barley MLA6 Immune Receptor in Association with Loss of NLR Protein. Mol Plant Microbe Interact 2022; 35:274-289. [PMID: 34889653 DOI: 10.1094/mpmi-08-21-0217-r] [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] [Indexed: 06/13/2023]
Abstract
The Mla (Mildew resistance locus a) of barley (Hordeum vulgare L.) is an effective model for cereal immunity against fungal pathogens. Like many resistance proteins, variants of the MLA coiled-coil nucleotide-binding leucine-rich repeat (CC-NLR) receptor often require the HRS complex (HSP90, RAR1, and SGT1) to function. However, functional analysis of Sgt1 has been particularly difficult, as deletions are often lethal. Recently, we identified rar3 (required for Mla6 resistance 3), an in-frame Sgt1ΔKL308-309 mutation in the SGT1-specific domain, that alters resistance conferred by MLA but without lethality. Here, we use autoactive MLA6 and recombinant yeast-two-hybrid strains with stably integrated HvRar1 and HvHsp90 to determine that this mutation weakens but does not entirely disrupt the interaction between SGT1 and MLA. This causes a concomitant reduction in MLA6 protein accumulation below the apparent threshold required for effective resistance. The ΔKL308-309 deletion had a lesser effect on intramolecular interactions than alanine or arginine substitutions, and MLA variants that display diminished interactions with SGT1 appear to be disproportionately affected by the SGT1ΔKL308-309 mutation. We hypothesize that those dimeric plant CC-NLRs that appear unaffected by Sgt1 silencing are those with the strongest intermolecular interactions with it. Combining our data with recent work in CC-NLRs, we propose a cyclical model of the MLA-HRS resistosome interactions.[Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2022.
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Affiliation(s)
- Antony V E Chapman
- Interdepartmental Genetics & Genomics, Iowa State University, Ames, IA 50011, U.S.A
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - J Mitch Elmore
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Maxwell McReynolds
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, U.S.A
- Interdepartmental Plant Biology, Iowa State University, Ames, IA 50011, U.S.A
| | - Justin W Walley
- Interdepartmental Genetics & Genomics, Iowa State University, Ames, IA 50011, U.S.A
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, U.S.A
- Interdepartmental Plant Biology, Iowa State University, Ames, IA 50011, U.S.A
| | - Roger P Wise
- Interdepartmental Genetics & Genomics, Iowa State University, Ames, IA 50011, U.S.A
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, U.S.A
- Corn Insects and Crop Genetics Research Unit, USDA-Agricultural Research Service, Ames, IA 50011, U.S.A
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10
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Clark NM, Elmore JM, Walley JW. To the proteome and beyond: advances in single-cell omics profiling for plant systems. Plant Physiol 2022; 188:726-737. [PMID: 35235661 PMCID: PMC8825333 DOI: 10.1093/plphys/kiab429] [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: 06/02/2021] [Accepted: 08/16/2021] [Indexed: 05/19/2023]
Abstract
Recent advances in single-cell proteomics for animal systems could be adapted for plants to increase our understanding of plant development, response to stimuli, and cell-to-cell signaling.
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Affiliation(s)
- Natalie M Clark
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | - James Mitch Elmore
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
- Author for communication:
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11
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McReynolds MR, Dash L, Montes C, Draves MA, Lang MG, Walley JW, Kelley DR. Temporal and spatial auxin responsive networks in maize primary roots. Quant Plant Biol 2022; 3:e21. [PMID: 37077976 PMCID: PMC10095944 DOI: 10.1017/qpb.2022.17] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 05/03/2023]
Abstract
Auxin is a key regulator of root morphogenesis across angiosperms. To better understand auxin-regulated networks underlying maize root development, we have characterized auxin-responsive transcription across two time points (30 and 120 min) and four regions of the primary root: the meristematic zone, elongation zone, cortex and stele. Hundreds of auxin-regulated genes involved in diverse biological processes were quantified in these different root regions. In general, most auxin-regulated genes are region unique and are predominantly observed in differentiated tissues compared with the root meristem. Auxin gene regulatory networks were reconstructed with these data to identify key transcription factors that may underlie auxin responses in maize roots. Additionally, Auxin-Response Factor subnetworks were generated to identify target genes that exhibit tissue or temporal specificity in response to auxin. These networks describe novel molecular connections underlying maize root development and provide a foundation for functional genomic studies in a key crop.
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Affiliation(s)
- Maxwell R. McReynolds
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa50011, USA
| | - Linkan Dash
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa50011, USA
| | - Christian Montes
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa50011, USA
| | - Melissa A. Draves
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa50011, USA
| | - Michelle G. Lang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa50011, USA
- Corteva Agriscience, Johnston, Iowa50131, USA
| | - Justin W. Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa50011, USA
- Authors for correspondence: D. R. Kelley and J. W. Walley, E-mail: ;
| | - Dior R. Kelley
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa50011, USA
- Authors for correspondence: D. R. Kelley and J. W. Walley, E-mail: ;
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12
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Wang P, Clark NM, Nolan TM, Song G, Whitham OG, Liao CY, Montes-Serey C, Bassham DC, Walley JW, Yin Y, Guo H. FERONIA functions through Target of Rapamycin (TOR) to negatively regulate autophagy. Front Plant Sci 2022; 13:961096. [PMID: 36082288 PMCID: PMC9446147 DOI: 10.3389/fpls.2022.961096] [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: 06/03/2022] [Accepted: 07/29/2022] [Indexed: 05/20/2023]
Abstract
FERONIA (FER) receptor kinase plays versatile roles in plant growth and development, biotic and abiotic stress responses, and reproduction. Autophagy is a conserved cellular recycling process that is critical for balancing plant growth and stress responses. Target of Rapamycin (TOR) has been shown to be a master regulator of autophagy. Our previous multi-omics analysis with loss-of-function fer-4 mutant implicated that FER functions in the autophagy pathway. We further demonstrated here that the fer-4 mutant displayed constitutive autophagy, and FER is required for TOR kinase activity measured by S6K1 phosphorylation and by root growth inhibition assay to TOR kinase inhibitor AZD8055. Taken together, our study provides a previously unknown mechanism by which FER functions through TOR to negatively regulate autophagy.
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Affiliation(s)
- Ping Wang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Natalie M. Clark
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | - Trevor M. Nolan
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | - Olivia G. Whitham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Ching-Yi Liao
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Christian Montes-Serey
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | - Diane C. Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Justin W. Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
- Plant Sciences Institute, Iowa State University, Ames, IA, United States
| | - Yanhai Yin
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
- Plant Sciences Institute, Iowa State University, Ames, IA, United States
| | - Hongqing Guo
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
- *Correspondence: Hongqing Guo,
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13
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Woodhouse MR, Sen S, Schott D, Portwood JL, Freeling M, Walley JW, Andorf CM, Schnable JC. qTeller: a tool for comparative multi-genomic gene expression analysis. Bioinformatics 2021; 38:236-242. [PMID: 34406385 DOI: 10.1093/bioinformatics/btab604] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/23/2021] [Accepted: 08/17/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Over the last decade, RNA-Seq whole-genome sequencing has become a widely used method for measuring and understanding transcriptome-level changes in gene expression. Since RNA-Seq is relatively inexpensive, it can be used on multiple genomes to evaluate gene expression across many different conditions, tissues and cell types. Although many tools exist to map and compare RNA-Seq at the genomics level, few web-based tools are dedicated to making data generated for individual genomic analysis accessible and reusable at a gene-level scale for comparative analysis between genes, across different genomes and meta-analyses. RESULTS To address this challenge, we revamped the comparative gene expression tool qTeller to take advantage of the growing number of public RNA-Seq datasets. qTeller allows users to evaluate gene expression data in a defined genomic interval and also perform two-gene comparisons across multiple user-chosen tissues. Though previously unpublished, qTeller has been cited extensively in the scientific literature, demonstrating its importance to researchers. Our new version of qTeller now supports multiple genomes for intergenomic comparisons, and includes capabilities for both mRNA and protein abundance datasets. Other new features include support for additional data formats, modernized interface and back-end database and an optimized framework for adoption by other organisms' databases. AVAILABILITY AND IMPLEMENTATION The source code for qTeller is open-source and available through GitHub (https://github.com/Maize-Genetics-and-Genomics-Database/qTeller). A maize instance of qTeller is available at the Maize Genetics and Genomics database (MaizeGDB) (https://qteller.maizegdb.org/), where we have mapped over 200 unique datasets from GenBank across 27 maize genomes. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Shatabdi Sen
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA
| | - David Schott
- Department of Computer Science, Iowa State University, Ames, IA 50011, USA
| | - John L Portwood
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA
| | - Michael Freeling
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Justin W Walley
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Carson M Andorf
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA.,Department of Computer Science, Iowa State University, Ames, IA 50011, USA
| | - James C Schnable
- Center for Plant Science Innovation & Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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14
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Wang P, Nolan TM, Clark NM, Jiang H, Montes-Serey C, Guo H, Bassham DC, Walley JW, Yin Y. The F-box E3 ubiquitin ligase BAF1 mediates the degradation of the brassinosteroid-activated transcription factor BES1 through selective autophagy in Arabidopsis. Plant Cell 2021; 33:3532-3554. [PMID: 34436598 PMCID: PMC8566207 DOI: 10.1093/plcell/koab210] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/14/2021] [Indexed: 05/02/2023]
Abstract
Brassinosteroids (BRs) regulate plant growth, development, and stress responses by activating the core transcription factor BRI1-EMS-SUPPRESSOR1 (BES1), whose degradation occurs through the proteasome and autophagy pathways. The E3 ubiquitin ligase(s) that modify BES1 for autophagy-mediated degradation remain to be fully defined. Here, we identified an F-box family E3 ubiquitin ligase named BES1-ASSOCIATED F-BOX1 (BAF1) in Arabidopsis thaliana. BAF1 interacts with BES1 and mediates its ubiquitination and degradation. Our genetic data demonstrated that BAF1 inhibits BR signaling in a BES1-dependent manner. Moreover, BAF1 targets BES1 for autophagic degradation in a selective manner. BAF1-triggered selective autophagy of BES1 depends on the ubiquitin binding receptor DOMINANT SUPPRESSOR OF KAR2 (DSK2). Sucrose starvation-induced selective autophagy of BES1, but not bulk autophagy, was significantly compromised in baf1 mutant and BAF1-ΔF (BAF1 F-box decoy) overexpression plants, but clearly increased by BAF1 overexpression. The baf1 and BAF1-ΔF overexpression plants had increased BR-regulated growth but were sensitive to long-term sucrose starvation, while BAF1 overexpression plants had decreased BR-regulated growth but were highly tolerant of sucrose starvation. Our results not only established BAF1 as an E3 ubiquitin ligase that targets BES1 for degradation through selective autophagy pathway, but also revealed a mechanism for plants to reduce growth during sucrose starvation.
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Affiliation(s)
- Ping Wang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Trevor M Nolan
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Natalie M Clark
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Hao Jiang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
| | | | - Hongqing Guo
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Diane C Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
- Plant Sciences Institutes, Iowa State University, Ames, Iowa 50011
| | - Yanhai Yin
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
- Plant Sciences Institutes, Iowa State University, Ames, Iowa 50011
- Author for correspondence:
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15
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Clark NM, Nolan TM, Wang P, Song G, Montes C, Valentine CT, Guo H, Sozzani R, Yin Y, Walley JW. Integrated omics networks reveal the temporal signaling events of brassinosteroid response in Arabidopsis. Nat Commun 2021; 12:5858. [PMID: 34615886 PMCID: PMC8494934 DOI: 10.1038/s41467-021-26165-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [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: 09/22/2020] [Accepted: 09/22/2021] [Indexed: 11/14/2022] Open
Abstract
Brassinosteroids (BRs) are plant steroid hormones that regulate cell division and stress response. Here we use a systems biology approach to integrate multi-omic datasets and unravel the molecular signaling events of BR response in Arabidopsis. We profile the levels of 26,669 transcripts, 9,533 protein groups, and 26,617 phosphorylation sites from Arabidopsis seedlings treated with brassinolide (BL) for six different lengths of time. We then construct a network inference pipeline called Spatiotemporal Clustering and Inference of Omics Networks (SC-ION) to integrate these data. We use our network predictions to identify putative phosphorylation sites on BES1 and experimentally validate their importance. Additionally, we identify BRONTOSAURUS (BRON) as a transcription factor that regulates cell division, and we show that BRON expression is modulated by BR-responsive kinases and transcription factors. This work demonstrates the power of integrative network analysis applied to multi-omic data and provides fundamental insights into the molecular signaling events occurring during BR response.
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Affiliation(s)
- Natalie M Clark
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Trevor M Nolan
- Department of Genetics, Developmental, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Ping Wang
- Department of Genetics, Developmental, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Christian Montes
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Conner T Valentine
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Hongqing Guo
- Department of Genetics, Developmental, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Yanhai Yin
- Department of Genetics, Developmental, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA.
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16
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Elmore JM, Griffin BD, Walley JW. Advances in functional proteomics to study plant-pathogen interactions. Curr Opin Plant Biol 2021; 63:102061. [PMID: 34102449 DOI: 10.1016/j.pbi.2021.102061] [Citation(s) in RCA: 7] [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: 03/04/2021] [Revised: 04/22/2021] [Accepted: 04/25/2021] [Indexed: 05/20/2023]
Abstract
Pathogen infection triggers complex signaling networks in plant cells that ultimately result in either susceptibility or resistance. We have made substantial progress in dissecting many of these signaling events, and it is becoming clear that changes in proteome composition and protein activity are major drivers of plant-microbe interactions. Here, we highlight different approaches to analyze the functional proteomes of hosts and pathogens and discuss how they have been used to further our understanding of plant disease. Global proteome profiling can quantify the dynamics of proteins, posttranslational modifications, and biological pathways that contribute to immune-related outcomes. In addition, emerging techniques such as enzyme activity-based profiling, proximity labeling, and kinase-substrate profiling are being used to dissect biochemical events that operate during infection. Finally, we discuss how these functional approaches can be integrated with other profiling data to gain a mechanistic, systems-level view of plant and pathogen signaling.
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Affiliation(s)
- James M Elmore
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50014, USA.
| | - Brianna D Griffin
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50014, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50014, USA.
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17
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Xiang L, Nolan TM, Bao Y, Elmore M, Tuel T, Gai J, Shah D, Wang P, Huser NM, Hurd AM, McLaughlin SA, Howell SH, Walley JW, Yin Y, Tang L. Robotic Assay for Drought (RoAD): an automated phenotyping system for brassinosteroid and drought responses. Plant J 2021; 107:1837-1853. [PMID: 34216161 DOI: 10.1111/tpj.15401] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 06/16/2021] [Accepted: 06/19/2021] [Indexed: 06/13/2023]
Abstract
Brassinosteroids (BRs) are a group of plant steroid hormones involved in regulating growth, development, and stress responses. Many components of the BR pathway have previously been identified and characterized. However, BR phenotyping experiments are typically performed in a low-throughput manner, such as on Petri plates. Additionally, the BR pathway affects drought responses, but drought experiments are time consuming and difficult to control. To mitigate these issues and increase throughput, we developed the Robotic Assay for Drought (RoAD) system to perform BR and drought response experiments in soil-grown Arabidopsis plants. RoAD is equipped with a robotic arm, a rover, a bench scale, a precisely controlled watering system, an RGB camera, and a laser profilometer. It performs daily weighing, watering, and imaging tasks and is capable of administering BR response assays by watering plants with Propiconazole (PCZ), a BR biosynthesis inhibitor. We developed image processing algorithms for both plant segmentation and phenotypic trait extraction to accurately measure traits including plant area, plant volume, leaf length, and leaf width. We then applied machine learning algorithms that utilize the extracted phenotypic parameters to identify image-derived traits that can distinguish control, drought-treated, and PCZ-treated plants. We carried out PCZ and drought experiments on a set of BR mutants and Arabidopsis accessions with altered BR responses. Finally, we extended the RoAD assays to perform BR response assays using PCZ in Zea mays (maize) plants. This study establishes an automated and non-invasive robotic imaging system as a tool to accurately measure morphological and growth-related traits of Arabidopsis and maize plants in 3D, providing insights into the BR-mediated control of plant growth and stress responses.
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Affiliation(s)
- Lirong Xiang
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Trevor M Nolan
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
- Plant Sciences Institutes, Iowa State University, Ames, IA, 50011, USA
| | - Yin Bao
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Mitch Elmore
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Taylor Tuel
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Jingyao Gai
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Dylan Shah
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Ping Wang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Nicole M Huser
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Ashley M Hurd
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Sean A McLaughlin
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Stephen H Howell
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
- Plant Sciences Institutes, Iowa State University, Ames, IA, 50011, USA
| | - Justin W Walley
- Plant Sciences Institutes, Iowa State University, Ames, IA, 50011, USA
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Yanhai Yin
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
- Plant Sciences Institutes, Iowa State University, Ames, IA, 50011, USA
| | - Lie Tang
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, 50011, USA
- Plant Sciences Institutes, Iowa State University, Ames, IA, 50011, USA
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18
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Dash L, McEwan RE, Montes C, Mejia L, Walley JW, Dilkes BP, Kelley DR. slim shady is a novel allele of PHYTOCHROME B present in the T-DNA line SALK_015201. Plant Direct 2021; 5:e00326. [PMID: 34136747 PMCID: PMC8197431 DOI: 10.1002/pld3.326] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/13/2021] [Accepted: 04/22/2021] [Indexed: 05/06/2023]
Abstract
Auxin is a hormone that is required for hypocotyl elongation during seedling development. In response to auxin, rapid changes in transcript and protein abundance occur in hypocotyls, and some auxin responsive gene expression is linked to hypocotyl growth. To functionally validate proteomic studies, a reverse genetics screen was performed on mutants in auxin-regulated proteins to identify novel regulators of plant growth. This uncovered a long hypocotyl mutant, which we called slim shady, in an annotated insertion line in IMMUNOREGULATORY RNA-BINDING PROTEIN (IRR). Overexpression of the IRR gene failed to rescue the slim shady phenotype and characterization of a second T-DNA allele of IRR found that it had a wild-type (WT) hypocotyl length. The slim shady mutant has an elevated expression of numerous genes associated with the brassinosteroid-auxin-phytochrome (BAP) regulatory module compared to WT, including transcription factors that regulate brassinosteroid, auxin, and phytochrome pathways. Additionally, slim shady seedlings fail to exhibit a strong transcriptional response to auxin. Using whole genome sequence data and genetic complementation analysis with SALK_015201C, we determined that a novel single nucleotide polymorphism in PHYTOCHROME B was responsible for the slim shady phenotype. This is predicted to induce a frameshift and premature stop codon at leucine 1125, within the histidine kinase-related domain of the carboxy terminus of PHYB, which is required for phytochrome signaling and function. Genetic complementation analyses with phyb-9 confirmed that slim shady is a mutant allele of PHYB. This study advances our understanding of the molecular mechanisms in seedling development, by furthering our understanding of how light signaling is linked to auxin-dependent cell elongation. Furthermore, this study highlights the importance of confirming the genetic identity of research material before attributing phenotypes to known mutations sourced from T-DNA stocks.
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Affiliation(s)
- Linkan Dash
- Department of GeneticsDevelopment and Cell BiologyIowa State UniversityAmesIAUSA
| | - Robert E. McEwan
- Center for Plant BiologyPurdue UniversityWest LafayettINUSA
- Department of Horticulture and Landscape ArchitecturePurdue UniversityWest LafayettINUSA
| | - Christian Montes
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Ludvin Mejia
- Department of GeneticsDevelopment and Cell BiologyIowa State UniversityAmesIAUSA
| | - Justin W. Walley
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Brian P. Dilkes
- Center for Plant BiologyPurdue UniversityWest LafayettINUSA
- Department of Horticulture and Landscape ArchitecturePurdue UniversityWest LafayettINUSA
- Department of BiochemistryPurdue UniversityWest LafayettINUSA
| | - Dior R. Kelley
- Department of GeneticsDevelopment and Cell BiologyIowa State UniversityAmesIAUSA
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Reem NT, Chambers L, Zhang N, Abdullah SF, Chen Y, Feng G, Gao S, Soto-Burgos J, Pogorelko G, Bassham DC, Anderson CT, Walley JW, Zabotina OA. Post-Synthetic Reduction of Pectin Methylesterification Causes Morphological Abnormalities and Alterations to Stress Response in Arabidopsis thaliana. Plants (Basel) 2020; 9:plants9111558. [PMID: 33198397 PMCID: PMC7697075 DOI: 10.3390/plants9111558] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/03/2020] [Accepted: 11/09/2020] [Indexed: 11/16/2022]
Abstract
Pectin is a critical component of the plant cell wall, supporting wall biomechanics and contributing to cell wall signaling in response to stress. The plant cell carefully regulates pectin methylesterification with endogenous pectin methylesterases (PMEs) and their inhibitors (PMEIs) to promote growth and protect against pathogens. We expressed Aspergillus nidulans pectin methylesterase (AnPME) in Arabidopsis thaliana plants to determine the impacts of methylesterification status on pectin function. Plants expressing AnPME had a roughly 50% reduction in methylester content compared with control plants. AnPME plants displayed a severe dwarf phenotype, including small, bushy rosettes and shorter roots. This phenotype was caused by a reduction in cell elongation. Cell wall composition was altered in AnPME plants, with significantly more arabinose and significantly less galacturonic acid, suggesting that plants actively monitor and compensate for altered pectin content. Cell walls of AnPME plants were more readily degraded by polygalacturonase (PG) alone but were less susceptible to treatment with a mixture of PG and PME. AnPME plants were insensitive to osmotic stress, and their susceptibility to Botrytis cinerea was comparable to wild type plants despite their compromised cell walls. This is likely due to upregulated expression of defense response genes observed in AnPME plants. These results demonstrate the importance of pectin in both normal growth and development, and in response to biotic and abiotic stresses.
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Affiliation(s)
- Nathan T. Reem
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA; (N.T.R.); (L.C.); (N.Z.); (S.F.A.); (G.P.)
| | - Lauran Chambers
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA; (N.T.R.); (L.C.); (N.Z.); (S.F.A.); (G.P.)
| | - Ning Zhang
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA; (N.T.R.); (L.C.); (N.Z.); (S.F.A.); (G.P.)
| | - Siti Farah Abdullah
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA; (N.T.R.); (L.C.); (N.Z.); (S.F.A.); (G.P.)
| | - Yintong Chen
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA; (Y.C.); (G.F.); (C.T.A.)
| | - Guanhua Feng
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA; (Y.C.); (G.F.); (C.T.A.)
| | - Song Gao
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA; (S.G.); (J.W.W.)
| | - Junmarie Soto-Burgos
- Department of Genetics, Development & Cell Biology, Iowa State University, Ames, IA 50011, USA; (J.S.-B.); (D.C.B.)
| | - Gennady Pogorelko
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA; (N.T.R.); (L.C.); (N.Z.); (S.F.A.); (G.P.)
| | - Diane C. Bassham
- Department of Genetics, Development & Cell Biology, Iowa State University, Ames, IA 50011, USA; (J.S.-B.); (D.C.B.)
| | - Charles T. Anderson
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA; (Y.C.); (G.F.); (C.T.A.)
| | - Justin W. Walley
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA; (S.G.); (J.W.W.)
| | - Olga A. Zabotina
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA; (N.T.R.); (L.C.); (N.Z.); (S.F.A.); (G.P.)
- Correspondence: ; Tel.: +1-515-294-6125
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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. 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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21
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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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22
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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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23
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Abstract
Proteins produce or regulate nearly every component of cells. Thus, the ability to quantitatively determine the protein abundance and posttranslational modification (PTM) state is a critical aspect toward our understanding of biological processes. In this chapter, we describe methods to globally quantify protein abundance and phosphorylation state using isobaric labeling with tandem mass tags followed by phosphopeptide enrichment.
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Affiliation(s)
- Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Christian Montes
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA.
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24
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Jia H, Song G, Werth EG, Walley JW, Hicks LM, Jones AM. Front Cover: Receptor‐Like Kinase Phosphorylation of Arabidopsis Heterotrimeric G‐Protein Gα ‐Subunit AtGPA1. Proteomics 2019. [DOI: 10.1002/pmic.201970211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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25
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Jia H, Song G, Werth EG, Walley JW, Hicks LM, Jones AM. Receptor-Like Kinase Phosphorylation of Arabidopsis Heterotrimeric G-Protein Gα -Subunit AtGPA1. Proteomics 2019; 19:e1900265. [PMID: 31693794 PMCID: PMC7014827 DOI: 10.1002/pmic.201900265] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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] [Received: 08/13/2019] [Revised: 10/04/2019] [Indexed: 01/07/2023]
Abstract
As molecular on-off switches, heterotrimeric G protein complexes, comprised of a Gα subunit and an obligate Gβγ dimer, transmit extracellular signals received by G protein-coupled receptors (GPCRs) to cytoplasmic targets that respond to biotic and abiotic stimuli. Signal transduction is modulated by phosphorylation of GPCRs and G protein complexes. In Arabidopsis thaliana, the Gα subunit AtGPA1 is phosphorylated by the receptor-like kinase (RLK) BRI1-associated Kinase 1 (BAK1), but the extent that other RLKs phosphorylates AtGPA1 is unknown. Twenty-two trans-phosphorylation sites on AtGPA1 are mapped by 12 RLKs hypothesized to act in the Arabidopsis G protein signaling pathway. Cis-phosphorylation sites are also identified on these RLKs, some newly shown to be dual specific kinases. Multiple sites are present in the core AtGPA1 functional units, including pSer52 and/or pThr53 of the conserved P-loop that directly binds nucleotide/phosphate, pThr164, and pSer175 from αE helix in the intramolecular domain interface for nucleotide exchange and GTP hydrolysis, and pThr193 and/or pThr194 in Switch I (SwI) that coordinates nucleotide exchange and protein partner binding. Several AtGPA1 S/T phosphorylation sites are potentially nucleotide-dependent phosphorylation patterns, such as Ser52/Thr53 in the P-loop and Thr193 and/or Thr194 in SwI.
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Affiliation(s)
- Haiyan Jia
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Emily G Werth
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alan M Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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Wu HYL, Song G, Walley JW, Hsu PY. The Tomato Translational Landscape Revealed by Transcriptome Assembly and Ribosome Profiling. Plant Physiol 2019; 181:367-380. [PMID: 31248964 PMCID: PMC6716236 DOI: 10.1104/pp.19.00541] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 06/10/2019] [Indexed: 05/14/2023]
Abstract
Recent applications of translational control in Arabidopsis (Arabidopsis thaliana) highlight the potential power of manipulating mRNA translation for crop improvement. However, to what extent translational regulation is conserved between Arabidopsis and other species is largely unknown, and the translatome of most crops remains poorly studied. Here, we combined de novo transcriptome assembly and ribosome profiling to study global mRNA translation in tomato (Solanum lycopersicum) roots. Exploiting features corresponding to active translation, we discovered widespread unannotated translation events, including 1,329 upstream open reading frames (uORFs) within the 5' untranslated regions of annotated coding genes and 354 small ORFs (sORFs) among unannotated transcripts. uORFs may repress translation of their downstream main ORFs, whereas sORFs may encode signaling peptides. Besides evolutionarily conserved sORFs, we uncovered 96 Solanaceae-specific sORFs, revealing the importance of studying translatomes directly in crops. Proteomic analysis confirmed that some of the unannotated ORFs generate stable proteins in planta. In addition to defining the translatome, our results reveal the global regulation by uORFs and microRNAs. Despite diverging over 100 million years ago, many translational features are well conserved between Arabidopsis and tomato. Thus, our approach provides a high-throughput method to discover unannotated ORFs, elucidates evolutionarily conserved and unique translational features, and identifies regulatory mechanisms hidden in a crop genome.
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Affiliation(s)
- Hsin-Yen Larry Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Polly Yingshan Hsu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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Clark NM, Shen Z, Briggs SP, Walley JW, Kelley DR. Front Cover: Auxin Induces Widespread Proteome Remodeling in Arabidopsis Seedlings. Proteomics 2019. [DOI: 10.1002/pmic.201970151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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28
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Clark NM, Shen Z, Briggs SP, Walley JW, Kelley DR. Auxin Induces Widespread Proteome Remodeling in Arabidopsis Seedlings. Proteomics 2019; 19:e1900199. [DOI: 10.1002/pmic.201900199] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/25/2019] [Indexed: 01/24/2023]
Affiliation(s)
- Natalie M. Clark
- Department of Plant Pathology and MicrobiologyIowa State University Ames IA 92093 USA
| | - Zhouxin Shen
- Section of Cell and Developmental BiologyUniversity of CaliforniaSan Diego La Jolla CA 92093 USA
| | - Steven P. Briggs
- Section of Cell and Developmental BiologyUniversity of CaliforniaSan Diego La Jolla CA 92093 USA
| | - Justin W. Walley
- Department of Plant Pathology and MicrobiologyIowa State University Ames IA 92093 USA
| | - Dior R. Kelley
- Department of Genetics, Development and Cell BiologyIowa State University Ames IA 50011 USA
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29
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Zhang Y, Song G, Lal NK, Nagalakshmi U, Li Y, Zheng W, Huang PJ, Branon TC, Ting AY, Walley JW, Dinesh-Kumar SP. TurboID-based proximity labeling reveals that UBR7 is a regulator of N NLR immune receptor-mediated immunity. Nat Commun 2019; 10:3252. [PMID: 31324801 PMCID: PMC6642208 DOI: 10.1038/s41467-019-11202-z] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [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: 11/16/2018] [Accepted: 07/01/2019] [Indexed: 11/25/2022] Open
Abstract
Nucleotide-binding leucine-rich repeat (NLR) immune receptors play a critical role in defence against pathogens in plants and animals. However, we know very little about NLR-interacting proteins and the mechanisms that regulate NLR levels. Here, we used proximity labeling (PL) to identify the proteome proximal to N, which is an NLR that confers resistance to Tobacco mosaic virus (TMV). Evaluation of different PL methods indicated that TurboID-based PL provides more efficient levels of biotinylation than BioID and BioID2 in plants. TurboID-based PL of N followed by quantitative proteomic analysis and genetic screening revealed multiple regulators of N-mediated immunity. Interestingly, a putative E3 ubiquitin ligase, UBR7, directly interacts with the TIR domain of N. UBR7 downregulation leads to an increased amount of N protein and enhanced TMV resistance. TMV-p50 effector disrupts the N-UBR7 interaction and relieves negative regulation of N. These findings demonstrate the utility of TurboID-based PL in plants and the N-interacting proteins we identified enhance our understanding of the mechanisms underlying NLR regulation.
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Affiliation(s)
- Yongliang Zhang
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, 95616, USA.
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Neeraj K Lal
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, 95616, USA
| | - Ugrappa Nagalakshmi
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, 95616, USA
| | - Yuanyuan Li
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, 95616, USA
| | - Wenjie Zheng
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, 95616, USA
| | - Pin-Jui Huang
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, 95616, USA
| | - Tess C Branon
- Departments of Genetics, Stanford University, Stanford, CA, 94305, USA
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Alice Y Ting
- Departments of Genetics, Stanford University, Stanford, CA, 94305, USA
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA.
| | - Savithramma P Dinesh-Kumar
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, 95616, USA.
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30
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Zhang J, Wu S, Boehlein SK, McCarty DR, Song G, Walley JW, Myers A, Settles AM. Maize defective kernel5 is a bacterial TamB homologue required for chloroplast envelope biogenesis. J Cell Biol 2019; 218:2638-2658. [PMID: 31235479 PMCID: PMC6683743 DOI: 10.1083/jcb.201807166] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 05/07/2019] [Accepted: 06/04/2019] [Indexed: 01/10/2023] Open
Abstract
Zhang et al. show that the maize dek5 locus is required for chloroplast envelope biogenesis and encodes a TamB-like protein. Bacterial TamB proteins facilitate insertion of β-barrel outer membrane proteins, indicating plastids have a conserved mechanism for envelope membrane biogenesis. Chloroplasts are of prokaryotic origin with a double-membrane envelope separating plastid metabolism from the cytosol. Envelope membrane proteins integrate chloroplasts with the cell, but envelope biogenesis mechanisms remain elusive. We show that maize defective kernel5 (dek5) is critical for envelope biogenesis. Amyloplasts and chloroplasts are larger and reduced in number in dek5 with multiple ultrastructural defects. The DEK5 protein is homologous to rice SSG4, Arabidopsis thaliana EMB2410/TIC236, and Escherichia coli tamB. TamB functions in bacterial outer membrane biogenesis. DEK5 is localized to the envelope with a topology analogous to TamB. Increased levels of soluble sugars in dek5 developing endosperm and elevated osmotic pressure in mutant leaf cells suggest defective intracellular solute transport. Proteomics and antibody-based analyses show dek5 reduces levels of Toc75 and chloroplast envelope transporters. Moreover, dek5 chloroplasts reduce inorganic phosphate uptake with at least an 80% reduction relative to normal chloroplasts. These data suggest that DEK5 functions in plastid envelope biogenesis to enable transport of metabolites and proteins.
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Affiliation(s)
- Junya Zhang
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL
| | - Shan Wu
- Horticultural Sciences Department, University of Florida, Gainesville, FL
| | - Susan K Boehlein
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL.,Horticultural Sciences Department, University of Florida, Gainesville, FL
| | - Donald R McCarty
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL.,Horticultural Sciences Department, University of Florida, Gainesville, FL
| | - Gaoyuan Song
- Plant Pathology and Microbiology, Iowa State University, Ames, IA
| | - Justin W Walley
- Plant Pathology and Microbiology, Iowa State University, Ames, IA
| | - Alan Myers
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA
| | - A Mark Settles
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL .,Horticultural Sciences Department, University of Florida, Gainesville, FL
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31
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Pu Y, Walley JW, Shen Z, Lang MG, Briggs SP, Estelle M, Kelley DR. Quantitative Early Auxin Root Proteomics Identifies GAUT10, a Galacturonosyltransferase, as a Novel Regulator of Root Meristem Maintenance. Mol Cell Proteomics 2019; 18:1157-1170. [PMID: 30918009 PMCID: PMC6553934 DOI: 10.1074/mcp.ra119.001378] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 02/14/2019] [Indexed: 11/25/2022] Open
Abstract
Auxin induces rapid gene expression changes throughout root development. How auxin-induced transcriptional responses relate to changes in protein abundance is not well characterized. This report identifies early auxin responsive proteins in roots at 30 min and 2 h after hormone treatment using a quantitative proteomics approach in which 3,514 proteins were reliably quantified. A comparison of the >100 differentially expressed proteins at each the time point showed limited overlap, suggesting a dynamic and transient response to exogenous auxin. Several proteins with established roles in auxin-mediated root development exhibited altered abundance, providing support for this approach. While novel targeted proteomics assays demonstrate that all six auxin receptors remain stable in response to hormone. Additionally, 15 of the top responsive proteins display root and/or auxin response phenotypes, demonstrating the validity of these differentially expressed proteins. Auxin signaling in roots dictates proteome reprogramming of proteins enriched for several gene ontology terms, including transcription, translation, protein localization, thigmatropism, and cell wall modification. In addition, we identified auxin-regulated proteins that had not previously been implicated in auxin response. For example, genetic studies of the auxin responsive protein galacturonosyltransferase 10 demonstrate that this enzyme plays a key role in root development. Altogether these data complement and extend our understanding of auxin response beyond that provided by transcriptome studies and can be used to uncover novel proteins that may mediate root developmental programs.
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Affiliation(s)
- Yunting Pu
- From the Departments of ‡Genetics, Development and Cell Biology
| | - Justin W Walley
- ¶Plant Pathology and Microbiology, Iowa State University, Ames, IA
| | - Zhouxin Shen
- §Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA
| | - Michelle G Lang
- From the Departments of ‡Genetics, Development and Cell Biology
| | - Steven P Briggs
- §Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA
| | - Mark Estelle
- §Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA
| | - Dior R Kelley
- From the Departments of ‡Genetics, Development and Cell Biology,
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32
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Abstract
The condition of the placenta is a determinant of the short- and long-term health of the mother and the fetus. However, critical processes occurring in early placental development, such as trophoblast invasion and establishment of placental metabolism, remain poorly understood. To gain a better understanding of the genes involved in regulating these processes, we utilized a multiomics approach, incorporating transcriptome, proteome, and phosphoproteome data generated from mouse placental tissue collected at two critical developmental time points. We found that incorporating information from both the transcriptome and proteome identifies genes associated with time point-specific biological processes, unlike using the proteome alone. We further inferred genes upregulated on the basis of the proteome data but not the transcriptome data at each time point, leading us to identify 27 genes that we predict to have a role in trophoblast migration or placental metabolism. Finally, using the phosphoproteome data set, we discovered novel phosphosites that may play crucial roles in the regulation of placental transcription factors. By generating the largest proteome and phosphoproteome data sets in the developing placenta, and integrating transcriptome analysis, we uncovered novel aspects of placental gene regulation.
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Affiliation(s)
- Majd Abdulghani
- Interdepartmental Genetics and Genomics , Iowa State University , Ames , Iowa 50011-1079 , United States.,Department of Genetics, Development, and Cell Biology , Iowa State University , Ames , Iowa 50011-1079 , United States
| | - Gaoyuan Song
- Department of Plant Pathology and Microbiology , Iowa State University , Ames , Iowa 50011-1079 , United States
| | - Haninder Kaur
- Department of Genetics, Development, and Cell Biology , Iowa State University , Ames , Iowa 50011-1079 , United States
| | - Justin W Walley
- Interdepartmental Genetics and Genomics , Iowa State University , Ames , Iowa 50011-1079 , United States.,Department of Plant Pathology and Microbiology , Iowa State University , Ames , Iowa 50011-1079 , United States
| | - Geetu Tuteja
- Interdepartmental Genetics and Genomics , Iowa State University , Ames , Iowa 50011-1079 , United States.,Department of Genetics, Development, and Cell Biology , Iowa State University , Ames , Iowa 50011-1079 , United States
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33
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Argueso CT, Assmann SM, Birnbaum KD, Chen S, Dinneny JR, Doherty CJ, Eveland AL, Friesner J, Greenlee VR, Law JA, Marshall‐Colón A, Mason GA, O'Lexy R, Peck SC, Schmitz RJ, Song L, Stern D, Varagona MJ, Walley JW, Williams CM. Directions for research and training in plant omics: Big Questions and Big Data. Plant Direct 2019; 3:e00133. [PMID: 31245771 PMCID: PMC6589541 DOI: 10.1002/pld3.133] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 03/21/2019] [Indexed: 05/04/2023]
Abstract
A key remit of the NSF-funded "Arabidopsis Research and Training for the 21st Century" (ART-21) Research Coordination Network has been to convene a series of workshops with community members to explore issues concerning research and training in plant biology, including the role that research using Arabidopsis thaliana can play in addressing those issues. A first workshop focused on training needs for bioinformatic and computational approaches in plant biology was held in 2016, and recommendations from that workshop have been published (Friesner et al., Plant Physiology, 175, 2017, 1499). In this white paper, we provide a summary of the discussions and insights arising from the second ART-21 workshop. The second workshop focused on experimental aspects of omics data acquisition and analysis and involved a broad spectrum of participants from academics and industry, ranging from graduate students through post-doctorates, early career and established investigators. Our hope is that this article will inspire beginning and established scientists, corporations, and funding agencies to pursue directions in research and training identified by this workshop, capitalizing on the reference species Arabidopsis thaliana and other valuable plant systems.
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Affiliation(s)
- Cristiana T. Argueso
- Department of Bioagricultural Sciences and Pest ManagementColorado State UniversityFort CollinsColorado
| | - Sarah M. Assmann
- Biology DepartmentPenn State UniversityUniversity ParkPennsylvania
| | - Kenneth D. Birnbaum
- Department of BiologyCenter for Genomics and Systems BiologyNew York UniversityNew YorkNew York
| | - Sixue Chen
- Department of BiologyGenetics InstitutePlant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleFlorida
- Proteomics and Mass SpectrometryInterdisciplinary Center for Biotechnology ResearchUniversity of FloridaGainesvilleFlorida
| | | | - Colleen J. Doherty
- Department of Molecular and Structural BiochemistryNorth Carolina State UniversityRaleighNorth Carolina
| | | | | | - Vanessa R. Greenlee
- International ProgramsCollege of Agriculture and Life SciencesCornell UniversityIthacaNew York
| | - Julie A. Law
- Plant Molecular and Cellular Biology LaboratorySalk Institute for Biological StudiesLa JollaCalifornia
- Division of Biological SciencesUniversity of California, San DiegoLa JollaCalifornia
| | - Amy Marshall‐Colón
- Department of Plant BiologyUniversity of Illinois Urbana‐ChampaignUrbanaIllinois
| | - Grace Alex Mason
- Department of Plant Biology and Genome CenterUC DavisDavisCalifornia
| | - Ruby O'Lexy
- Coriell Institute for Medical ResearchCamdenNew Jersey
| | - Scott C. Peck
- Division of BiochemistryChristopher S. Bond Life Sciences CenterInterdisciplinary Plant GroupUniversity of MissouriColumbiaMissouri
| | | | - Liang Song
- Department of BotanyThe University of British ColumbiaVancouverBritish ColumbiaCanada
| | | | | | - Justin W. Walley
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIowa
| | - Cranos M. Williams
- Department of Electrical and Computer EngineeringNorth Carolina State UniversityRaleighNorth Carolina
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34
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Song G, Brachova L, Nikolau BJ, Jones AM, Walley JW. Heterotrimeric G-Protein-Dependent Proteome and Phosphoproteome in Unstimulated Arabidopsis Roots. Proteomics 2018; 18:e1800323. [PMID: 30407730 PMCID: PMC6298806 DOI: 10.1002/pmic.201800323] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [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] [Received: 08/25/2018] [Revised: 10/09/2018] [Indexed: 12/19/2022]
Abstract
The G-protein complex is a cytoplasmic on-off molecular switch that is set by plasma membrane receptors that activate upon binding of its cognate extracellular agonist. In animals, the default setting is the "off" resting state, while in plants, the default state is constitutively "on" but repressed by a plasma membrane receptor-like protein. De-repression appears to involve specific phosphorylation of key elements of the G-protein complex and possibly target proteins that are positioned downstream of this complex. To address this possibility, protein abundance and phosphorylation state are quantified in wild type and G-protein deficient Arabidopsis roots in the unstimulated resting state. A total of 3246 phosphorylated and 8141 non-modified protein groups are identified. It has been found that 428 phosphorylation sites decrease and 509 sites increase in abundance in the G-protein quadrupole mutant lacking an operable G-protein-complex. Kinases with known roles in G-protein signaling including MAP KINASE 6 and FERONIA are differentially phosphorylated along with many other proteins now implicated in the control of G-protein signaling. Taken together, these datasets will enable the discovery of novel proteins and biological processes dependent on G-protein signaling.
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Affiliation(s)
- Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA USA
| | - Libuse Brachova
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Basil J. Nikolau
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Alan M. Jones
- Department of Biology and Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Justin W. Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA USA
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35
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Guo H, Nolan TM, Song G, Liu S, Xie Z, Chen J, Schnable PS, Walley JW, Yin Y. FERONIA Receptor Kinase Contributes to Plant Immunity by Suppressing Jasmonic Acid Signaling in Arabidopsis thaliana. Curr Biol 2018; 28:3316-3324.e6. [PMID: 30270181 DOI: 10.1016/j.cub.2018.07.078] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 06/28/2018] [Accepted: 07/30/2018] [Indexed: 11/30/2022]
Abstract
Bacterial pathogens use effectors and phytotoxins to facilitate infection of host plants. Coronatine (COR) is one of the phytotoxins produced in bacterial pathogens, such as Pseudomonas syringae pv. tomato DC3000 (pst DC3000). COR structurally and functionally mimics the active form of the plant hormone jasmonic acid (JA), JA-isoleucine (JA-Ile), and can hijack the host JA-signaling pathway to achieve host disease susceptibility [1]. COR utilizes the transcription factor MYC2, a master regulator of JA signaling, to activate NAC transcription factors, which functions to inhibit accumulation of salicylic acid (SA) and thus compromise host immunity [2]. It has been demonstrated that SA can antagonize JA signaling through NONEXPRESSOR of PATHOGENESIS-RELATED GENE1 (NPR1) [3] and downstream transcription factors TGAs [4] and WRKYs [5, 6]. However, the detailed mechanism by which host plants counteract COR-mediated susceptibility is largely unknown. Here, we show that the receptor kinase FERONIA (FER) functions to inhibit JA and COR signaling by phosphorylating and destabilizing MYC2, thereby positively regulating immunity. Conversely, the peptide ligand RALF23 acts through FER to stabilize MYC2 and elevate JA signaling, negatively contributing to plant immunity. Our results establish the RALF23-FER-MYC2 signaling module and provide a previously unknown mechanism by which host plants utilize FER signaling to counteract COR-mediated host disease susceptibility.
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Affiliation(s)
- Hongqing Guo
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA.
| | - Trevor M Nolan
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Sanzhen Liu
- Department of Agronomy, Iowa State University, Ames, IA, USA; Data2Bio, Ames, IA 50011-3650, USA
| | - Zhouli Xie
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Jiani Chen
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Patrick S Schnable
- Department of Agronomy, Iowa State University, Ames, IA, USA; Data2Bio, Ames, IA 50011-3650, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Yanhai Yin
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA.
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36
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Song G, Hsu PY, Walley JW. Assessment and Refinement of Sample Preparation Methods for Deep and Quantitative Plant Proteome Profiling. Proteomics 2018; 18:e1800220. [PMID: 30035338 DOI: 10.1002/pmic.201800220] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 06/28/2018] [Indexed: 12/20/2022]
Abstract
A major challenge in the field of proteomics is obtaining high-quality peptides for comprehensive proteome profiling by LC-MS. Here, evaluation and modification of a range of sample preparation methods using photosynthetically active Arabidopsis leaf tissue are done. It was found that inclusion of filter-aided sample preparation (FASP) based on filter digestion improves all protein extraction methods tested. Ultimately, a detergent-free urea-FASP approach that enables deep and robust quantification of leaf and root proteomes is shown. For example, from 4-day-old leaf tissue, up to 11 690 proteins were profiled from a single sample replicate. This method should be broadly applicable to researchers working with difficult to process plant samples.
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Affiliation(s)
- Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Polly Yingshan Hsu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48823, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
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37
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Song G, McReynolds MR, Walley JW. Sample Preparation Protocols for Protein Abundance, Acetylome, and Phosphoproteome Profiling of Plant Tissues. Methods Mol Biol 2017; 1610:123-133. [PMID: 28439861 DOI: 10.1007/978-1-4939-7003-2_9] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Peptide mass spectrometry is an invaluable technique to globally quantify the proteome. Central to proteome profiling are efficient methods to extract proteins, digest proteins into peptides, and enrich for posttranslationally modified peptides prior to mass spectrometry. In this chapter, we describe methods to extract proteins, process them into peptides, and optionally enrich for phospho- and acetyl-peptides prior to analysis by mass spectrometry.
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Affiliation(s)
- Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, 43 Bessey, Ames, IA, 50011, USA
| | - Maxwell R McReynolds
- Department of Plant Pathology and Microbiology, Iowa State University, 43 Bessey, Ames, IA, 50011, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, 43 Bessey, Ames, IA, 50011, USA.
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38
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Walley JW, Sartor RC, Shen Z, Schmitz RJ, Wu KJ, Urich MA, Nery JR, Smith LG, Schnable JC, Ecker JR, Briggs SP. Integration of omic networks in a developmental atlas of maize. Science 2016; 353:814-8. [PMID: 27540173 DOI: 10.1126/science.aag1125] [Citation(s) in RCA: 273] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/25/2016] [Indexed: 12/23/2022]
Abstract
Coexpression networks and gene regulatory networks (GRNs) are emerging as important tools for predicting functional roles of individual genes at a system-wide scale. To enable network reconstructions, we built a large-scale gene expression atlas composed of 62,547 messenger RNAs (mRNAs), 17,862 nonmodified proteins, and 6227 phosphoproteins harboring 31,595 phosphorylation sites quantified across maize development. Networks in which nodes are genes connected on the basis of highly correlated expression patterns of mRNAs were very different from networks that were based on coexpression of proteins. Roughly 85% of highly interconnected hubs were not conserved in expression between RNA and protein networks. However, networks from either data type were enriched in similar ontological categories and were effective in predicting known regulatory relationships. Integration of mRNA, protein, and phosphoprotein data sets greatly improved the predictive power of GRNs.
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Affiliation(s)
- Justin W Walley
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA. Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Ryan C Sartor
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Zhouxin Shen
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Robert J Schmitz
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA. Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Kevin J Wu
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Mark A Urich
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA. Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Joseph R Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Laurie G Smith
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA
| | - Joseph R Ecker
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA. Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA. Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Steven P Briggs
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.
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39
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Abstract
Pathogen infection triggers complex molecular perturbations within host cells that results in either resistance or susceptibility. Protein acetylation is an emerging biochemical modification that appears to play central roles during host-pathogen interactions. To date, research in this area has focused on two main themes linking protein acetylation to plant immune signaling. Firstly, it has been established that proper gene expression during defense responses requires modulation of histone acetylation within target gene promoter regions. Second, some pathogens can deliver effector molecules that encode acetyltransferases directly within the host cell to modify acetylation of specific host proteins. Collectively these findings suggest that the acetylation level for a range of host proteins may be modulated to alter the outcome of pathogen infection. This review will focus on summarizing our current understanding of the roles of protein acetylation in plant defense and highlight the utility of proteomics approaches to uncover the complete repertoire of acetylation changes triggered by pathogen infection.
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40
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Abstract
One of the objectives of genome science is the discovery and accurate annotation of all protein-coding genes. Proteogenomics has emerged as a methodology that provides orthogonal information to traditional forms of evidence used for genome annotation. By this method, peptides that are identified via tandem mass spectrometry are used to refine protein-coding gene models. Namely, these peptides are used to confirm the translation of predicted protein-coding genes, as evidence of novel genes or for correction of current gene models. Proteogenomics requires deep and broad sampling of the proteome in order to generate sufficient numbers of unique peptides. Therefore, we propose that proteogenomic projects are designed so that the generated peptides can also be used to create a comprehensive protein atlas that quantitatively catalogues protein abundance changes during development and in response to environmental stimulus.
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41
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Marcon C, Malik WA, Walley JW, Shen Z, Paschold A, Smith LG, Piepho HP, Briggs SP, Hochholdinger F. A high-resolution tissue-specific proteome and phosphoproteome atlas of maize primary roots reveals functional gradients along the root axes. Plant Physiol 2015; 168:233-46. [PMID: 25780097 PMCID: PMC4424028 DOI: 10.1104/pp.15.00138] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 03/14/2015] [Indexed: 05/18/2023]
Abstract
A high-resolution proteome and phosphoproteome atlas of four maize (Zea mays) primary root tissues, the cortex, stele, meristematic zone, and elongation zone, was generated. High-performance liquid chromatography coupled with tandem mass spectrometry identified 11,552 distinct nonmodified and 2,852 phosphorylated proteins across the four root tissues. Two gradients reflecting the abundance of functional protein classes along the longitudinal root axis were observed. While the classes RNA, DNA, and protein peaked in the meristematic zone, cell wall, lipid metabolism, stress, transport, and secondary metabolism culminated in the differentiation zone. Functional specialization of tissues is underscored by six of 10 cortex-specific proteins involved in flavonoid biosynthesis. Comparison of this data set with high-resolution seed and leaf proteome studies revealed 13% (1,504/11,552) root-specific proteins. While only 23% of the 1,504 root-specific proteins accumulated in all four root tissues, 61% of all 11,552 identified proteins accumulated in all four root tissues. This suggests a much higher degree of tissue-specific functionalization of root-specific proteins. In summary, these data illustrate the remarkable plasticity of the proteomic landscape of maize primary roots and thus provide a starting point for gaining a better understanding of their tissue-specific functions.
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Affiliation(s)
- Caroline Marcon
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany (C.M., A.P., F.H.);Institute of Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.); andSection of Cell and Developmental Biology, University of California-San Diego, La Jolla, California 92093 (J.W.W., Z.S., L.G.S., S.P.B.)
| | - Waqas Ahmed Malik
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany (C.M., A.P., F.H.);Institute of Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.); andSection of Cell and Developmental Biology, University of California-San Diego, La Jolla, California 92093 (J.W.W., Z.S., L.G.S., S.P.B.)
| | - Justin W Walley
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany (C.M., A.P., F.H.);Institute of Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.); andSection of Cell and Developmental Biology, University of California-San Diego, La Jolla, California 92093 (J.W.W., Z.S., L.G.S., S.P.B.)
| | - Zhouxin Shen
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany (C.M., A.P., F.H.);Institute of Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.); andSection of Cell and Developmental Biology, University of California-San Diego, La Jolla, California 92093 (J.W.W., Z.S., L.G.S., S.P.B.)
| | - Anja Paschold
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany (C.M., A.P., F.H.);Institute of Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.); andSection of Cell and Developmental Biology, University of California-San Diego, La Jolla, California 92093 (J.W.W., Z.S., L.G.S., S.P.B.)
| | - Laurie G Smith
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany (C.M., A.P., F.H.);Institute of Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.); andSection of Cell and Developmental Biology, University of California-San Diego, La Jolla, California 92093 (J.W.W., Z.S., L.G.S., S.P.B.)
| | - Hans-Peter Piepho
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany (C.M., A.P., F.H.);Institute of Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.); andSection of Cell and Developmental Biology, University of California-San Diego, La Jolla, California 92093 (J.W.W., Z.S., L.G.S., S.P.B.)
| | - Steven P Briggs
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany (C.M., A.P., F.H.);Institute of Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.); andSection of Cell and Developmental Biology, University of California-San Diego, La Jolla, California 92093 (J.W.W., Z.S., L.G.S., S.P.B.)
| | - Frank Hochholdinger
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany (C.M., A.P., F.H.);Institute of Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.); andSection of Cell and Developmental Biology, University of California-San Diego, La Jolla, California 92093 (J.W.W., Z.S., L.G.S., S.P.B.)
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Castellana NE, Shen Z, He Y, Walley JW, Cassidy CJ, Briggs SP, Bafna V. An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays. Mol Cell Proteomics 2013; 13:157-67. [PMID: 24142994 DOI: 10.1074/mcp.m113.031260] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
New technologies in genomics and proteomics have influenced the emergence of proteogenomics, a field at the confluence of genomics, transcriptomics, and proteomics. First generation proteogenomic toolkits employ peptide mass spectrometry to identify novel protein coding regions. We extend first generation proteogenomic tools to achieve greater accuracy and enable the analysis of large, complex genomes. We apply our pipeline to Zea mays, which has a genome comparable in size to human. Our pipeline begins with the comparison of mass spectra to a putative translation of the genome. We select novel peptides, those that match a region of the genome that was not previously known to be protein coding, for grouping into refinement events. We present a novel, probabilistic framework for evaluating the accuracy of each event. Our calculated event probability, or eventProb, considers the number of supporting peptides and spectra, and the quality of each supporting peptide-spectrum match. Our pipeline predicts 165 novel protein-coding genes and proposes updated models for 741 additional genes.
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Affiliation(s)
- Natalie E Castellana
- Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92092
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Walley JW, Kliebenstein DJ, Bostock RM, Dehesh K. Fatty acids and early detection of pathogens. Curr Opin Plant Biol 2013; 16:520-6. [PMID: 23845737 DOI: 10.1016/j.pbi.2013.06.011] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 06/11/2013] [Accepted: 06/13/2013] [Indexed: 05/20/2023]
Abstract
Early in interactions between plants and pathogens, plants recognize molecular signatures in microbial cells, triggering a form of immunity that may help resist infection and colonization by pathogens. Diverse molecules provide these molecular signatures, called pathogen-associated molecular patterns (PAMPs), including proteins, polysaccharides, and lipids. Before and concurrent with the onset of PAMP-triggered immunity, there are alterations in plant membrane lipid composition, modification of membrane fluidity through desaturase-mediated changes in unsaturated fatty acid levels, and enzymatic and non-enzymatic genesis of bioactive lipid mediators such as oxylipins. These complex lipid changes produce a myriad of potential molecular signatures that are beginning to be found to have key roles in the regulation of transcriptional networks. Further, research on fatty acid action in various biological contexts, including plant-pathogen interactions and stress network signaling, is needed to fully understand fatty acids as regulatory signals that transcend their established role in membrane structure and function.
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Affiliation(s)
- Justin W Walley
- Department of Plant Biology, University of California, Davis, CA 95616, USA
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Savchenko T, Walley JW, Chehab EW, Xiao Y, Kaspi R, Pye MF, Mohamed ME, Lazarus CM, Bostock RM, Dehesh K. Arachidonic acid: an evolutionarily conserved signaling molecule modulates plant stress signaling networks. Plant Cell 2010; 22:3193-205. [PMID: 20935246 PMCID: PMC2990140 DOI: 10.1105/tpc.110.073858] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Revised: 09/16/2010] [Accepted: 09/22/2010] [Indexed: 05/18/2023]
Abstract
Fatty acid structure affects cellular activities through changes in membrane lipid composition and the generation of a diversity of bioactive derivatives. Eicosapolyenoic acids are released into plants upon infection by oomycete pathogens, suggesting they may elicit plant defenses. We exploited transgenic Arabidopsis thaliana plants (designated EP) producing eicosadienoic, eicosatrienoic, and arachidonic acid (AA), aimed at mimicking pathogen release of these compounds. We also examined their effect on biotic stress resistance by challenging EP plants with fungal, oomycete, and bacterial pathogens and an insect pest. EP plants exhibited enhanced resistance to all biotic challenges, except they were more susceptible to bacteria than the wild type. Levels of jasmonic acid (JA) were elevated and levels of salicylic acid (SA) were reduced in EP plants. Altered expression of JA and SA pathway genes in EP plants shows that eicosapolyenoic acids effectively modulate stress-responsive transcriptional networks. Exogenous application of various fatty acids to wild-type and JA-deficient mutants confirmed AA as the signaling molecule. Moreover, AA treatment elicited heightened expression of general stress-responsive genes. Importantly, tomato (Solanum lycopersicum) leaves treated with AA exhibited reduced susceptibility to Botrytis cinerea infection, confirming AA signaling in other plants. These studies support the role of AA, an ancient metazoan signaling molecule, in eliciting plant stress and defense signaling networks.
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Affiliation(s)
- Tatyana Savchenko
- Department of Plant Biology, University of California, Davis, California 95616
| | - Justin W. Walley
- Department of Plant Biology, University of California, Davis, California 95616
- Department of Biological Sciences, University of California, San Diego, California 92093-0380
| | - E. Wassim Chehab
- Department of Plant Biology, University of California, Davis, California 95616
| | - Yanmei Xiao
- Department of Plant Biology, University of California, Davis, California 95616
| | - Roy Kaspi
- Department of Plant Biology, University of California, Davis, California 95616
| | - Matthew F. Pye
- Department of Plant Pathology, University of California, Davis, California 95616
| | - Maged E. Mohamed
- School of Biological Sciences, University of Bristol, Bristol BS8 1UG, United Kingdom
| | - Colin M. Lazarus
- School of Biological Sciences, University of Bristol, Bristol BS8 1UG, United Kingdom
| | - Richard M. Bostock
- Department of Plant Pathology, University of California, Davis, California 95616
| | - Katayoon Dehesh
- Department of Plant Biology, University of California, Davis, California 95616
- Address correspondence to
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45
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Walley JW, Kelley DR, Savchenko T, Dehesh K. Investigating the function of CAF1 deadenylases during plant stress responses. Plant Signal Behav 2010; 5:802-805. [PMID: 20421740 PMCID: PMC3115028 DOI: 10.4161/psb.5.7.11578] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [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: 02/18/2010] [Accepted: 02/18/2010] [Indexed: 05/29/2023]
Abstract
Alteration of gene expression plays a central role in the transmission of developmental and environmental signals. The steady-state transcript level within a cell is determined by the combination of the rate synthesis and the rate of degradation. While altering the rate of mRNA turnover is known to provide a rapid mechanism to reprogram transcript levels, research has largely focused on changes in transcriptional regulation as a mechanism to control mRNA levels. However, recent studies have begun to explore the role of mRNA decay in reprogramming the transcriptome.
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Affiliation(s)
- Justin W Walley
- Division of Biological Sciences; University of California at San Diego; La Jolla, CA USA
| | - Dior R Kelley
- Plant Molecular and Cellular Biology Laboratory; Salk Institute for Biological Sciences; La Jolla, CA USA
| | - Tatyana Savchenko
- Department of Plant Biology; University of California at Davis; Davis, CA USA
| | - Katayoon Dehesh
- Department of Plant Biology; University of California at Davis; Davis, CA USA
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Abstract
As sessile organisms plants must cope with ever changing environmental conditions. To survive plants have evolved elaborate mechanisms to perceive and rapidly respond to a diverse range of abiotic and biotic stresses. Central to this response is the ability to modulate gene expression at both the transcriptional and post-transcriptional levels. This review will focus on recent progress that has been made towards understanding the rapid reprogramming of the transcriptome that occurs in response to stress as well as emerging mechanisms underpinning the reprogramming of gene expression in response to stress.
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Affiliation(s)
- Justin W Walley
- Department of Plant Biology, University of California, Davis, CA 95616, USA
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Walley JW, Kelley DR, Nestorova G, Hirschberg DL, Dehesh K. Arabidopsis deadenylases AtCAF1a and AtCAF1b play overlapping and distinct roles in mediating environmental stress responses. Plant Physiol 2010; 152:866-75. [PMID: 19955262 PMCID: PMC2815882 DOI: 10.1104/pp.109.149005] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Accepted: 11/25/2009] [Indexed: 05/19/2023]
Abstract
To maintain homeostasis in an ever-changing environment organisms have evolved mechanisms to reprogram gene expression. One central mechanism regulating gene expression is messenger RNA (mRNA) degradation, which is initiated by poly(A) tail shortening (deadenylation). The carbon catabolite repressor 4-CCR4 associated factor1 (CCR4-CAF1) complex is the major enzyme complex that catalyzes mRNA deadenylation and is conserved among eukaryotes. However, the components and functions of this global regulatory complex have not been well characterized in plants. Here we investigate the CAF1 family in Arabidopsis (Arabidopsis thaliana). We identify 11 AtCAF1 homologs and show that a subset of these genes are responsive to mechanical wounding, among them are AtCAF1a and AtCAF1b whose expression levels are rapidly and transiently induced by wounding. The differential expression profiles of the various AtCAF1s suggest that not all AtCAF1 genes are involved in stress-responsive regulation of transcript levels. Comparison of misexpressed genes identified via transcript profiling of Atcaf1a and Atcaf1b mutants at different time points before and after wounding suggests that AtCAF1a and AtCAF1b target shared and unique transcripts for deadenylation with temporal specificity. Consistent with the AtPI4Kgamma3 transcript exhibiting the largest increase in abundance in Atcaf1b, AtCAF1b targets AtPI4Kgamma3 mRNA for deadenylation. Stress-tolerance assays demonstrate that AtCAF1a and AtCAF1b are involved in mediating abiotic stress responses. However, AtCAF1a and AtCAF1b are not functionally redundant in all cases, nor are they essential for all environmental stresses. These findings demonstrate that these closely related proteins exhibit overlapping and distinct roles with respect to mRNA deadenylation and mediation of stress responses.
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Walley JW, Rowe HC, Xiao Y, Chehab EW, Kliebenstein DJ, Wagner D, Dehesh K. The chromatin remodeler SPLAYED regulates specific stress signaling pathways. PLoS Pathog 2008; 4:e1000237. [PMID: 19079584 PMCID: PMC2588541 DOI: 10.1371/journal.ppat.1000237] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [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: 07/07/2008] [Accepted: 11/12/2008] [Indexed: 11/19/2022] Open
Abstract
Organisms are continuously exposed to a myriad of environmental stresses. Central to an organism's survival is the ability to mount a robust transcriptional response to the imposed stress. An emerging mechanism of transcriptional control involves dynamic changes in chromatin structure. Alterations in chromatin structure are brought about by a number of different mechanisms, including chromatin modifications, which covalently modify histone proteins; incorporation of histone variants; and chromatin remodeling, which utilizes ATP hydrolysis to alter histone-DNA contacts. While considerable insight into the mechanisms of chromatin remodeling has been gained, the biological role of chromatin remodeling complexes beyond their function as regulators of cellular differentiation and development has remained poorly understood. Here, we provide genetic, biochemical, and biological evidence for the critical role of chromatin remodeling in mediating plant defense against specific biotic stresses. We found that the Arabidopsis SWI/SNF class chromatin remodeling ATPase SPLAYED (SYD) is required for the expression of selected genes downstream of the jasmonate (JA) and ethylene (ET) signaling pathways. SYD is also directly recruited to the promoters of several of these genes. Furthermore, we show that SYD is required for resistance against the necrotrophic pathogen Botrytis cinerea but not the biotrophic pathogen Pseudomonas syringae. These findings demonstrate not only that chromatin remodeling is required for selective pathogen resistance, but also that chromatin remodelers such as SYD can regulate specific pathways within biotic stress signaling networks.
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Affiliation(s)
- Justin W. Walley
- Department of Plant Biology, University of California, Davis, California, United States of America
| | - Heather C. Rowe
- Department of Plant Sciences, University of California, Davis, United States of America
| | - Yanmei Xiao
- Department of Plant Biology, University of California, Davis, California, United States of America
| | - E. Wassim Chehab
- Department of Plant Biology, University of California, Davis, California, United States of America
| | | | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Katayoon Dehesh
- Department of Plant Biology, University of California, Davis, California, United States of America
- * E-mail:
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49
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Walley JW, Coughlan S, Hudson ME, Covington MF, Kaspi R, Banu G, Harmer SL, Dehesh K. Mechanical stress induces biotic and abiotic stress responses via a novel cis-element. PLoS Genet 2007. [PMID: 17953483 DOI: 10.1131/journal.pgen.0030172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2023] Open
Abstract
Plants are continuously exposed to a myriad of abiotic and biotic stresses. However, the molecular mechanisms by which these stress signals are perceived and transduced are poorly understood. To begin to identify primary stress signal transduction components, we have focused on genes that respond rapidly (within 5 min) to stress signals. Because it has been hypothesized that detection of physical stress is a mechanism common to mounting a response against a broad range of environmental stresses, we have utilized mechanical wounding as the stress stimulus and performed whole genome microarray analysis of Arabidopsis thaliana leaf tissue. This led to the identification of a number of rapid wound responsive (RWR) genes. Comparison of RWR genes with published abiotic and biotic stress microarray datasets demonstrates a large overlap across a wide range of environmental stresses. Interestingly, RWR genes also exhibit a striking level and pattern of circadian regulation, with induced and repressed genes displaying antiphasic rhythms. Using bioinformatic analysis, we identified a novel motif overrepresented in the promoters of RWR genes, herein designated as the Rapid Stress Response Element (RSRE). We demonstrate in transgenic plants that multimerized RSREs are sufficient to confer a rapid response to both biotic and abiotic stresses in vivo, thereby establishing the functional involvement of this motif in primary transcriptional stress responses. Collectively, our data provide evidence for a novel cis-element that is distributed across the promoters of an array of diverse stress-responsive genes, poised to respond immediately and coordinately to stress signals. This structure suggests that plants may have a transcriptional network resembling the general stress signaling pathway in yeast and that the RSRE element may provide the key to this coordinate regulation.
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Affiliation(s)
- Justin W Walley
- Section of Plant Biology, University of California Davis, Davis, California, USA
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50
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Walley JW, Coughlan S, Hudson ME, Covington MF, Kaspi R, Banu G, Harmer SL, Dehesh K. Mechanical stress induces biotic and abiotic stress responses via a novel cis-element. PLoS Genet 2007; 3:1800-12. [PMID: 17953483 PMCID: PMC2039767 DOI: 10.1371/journal.pgen.0030172] [Citation(s) in RCA: 173] [Impact Index Per Article: 10.2] [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: 07/04/2007] [Accepted: 08/22/2007] [Indexed: 12/25/2022] Open
Abstract
Plants are continuously exposed to a myriad of abiotic and biotic stresses. However, the molecular mechanisms by which these stress signals are perceived and transduced are poorly understood. To begin to identify primary stress signal transduction components, we have focused on genes that respond rapidly (within 5 min) to stress signals. Because it has been hypothesized that detection of physical stress is a mechanism common to mounting a response against a broad range of environmental stresses, we have utilized mechanical wounding as the stress stimulus and performed whole genome microarray analysis of Arabidopsis thaliana leaf tissue. This led to the identification of a number of rapid wound responsive (RWR) genes. Comparison of RWR genes with published abiotic and biotic stress microarray datasets demonstrates a large overlap across a wide range of environmental stresses. Interestingly, RWR genes also exhibit a striking level and pattern of circadian regulation, with induced and repressed genes displaying antiphasic rhythms. Using bioinformatic analysis, we identified a novel motif overrepresented in the promoters of RWR genes, herein designated as the Rapid Stress Response Element (RSRE). We demonstrate in transgenic plants that multimerized RSREs are sufficient to confer a rapid response to both biotic and abiotic stresses in vivo, thereby establishing the functional involvement of this motif in primary transcriptional stress responses. Collectively, our data provide evidence for a novel cis-element that is distributed across the promoters of an array of diverse stress-responsive genes, poised to respond immediately and coordinately to stress signals. This structure suggests that plants may have a transcriptional network resembling the general stress signaling pathway in yeast and that the RSRE element may provide the key to this coordinate regulation. Plants are sessile organisms constantly challenged by a wide spectrum of biotic and abiotic stresses. These stresses cause considerable losses in crop yields worldwide, while the demand for food and energy is on the rise. Understanding the molecular mechanisms driving stress responses is crucial to devising targeted strategies to engineer stress-tolerant plants. To identify primary stress-responsive genes we examined the transcriptional profile of plants after mechanical wounding, which was used as a brief, inductive stimulus. Comparison of the ensemble of rapid wound response transcripts with published transcript profiles revealed a notable overlap with biotic and abiotic stress-responsive genes. Additional quantitative analyses of selected genes over a wounding time-course enabled classification into two groups: transient and stably expressed. Bioinformatic analysis of rapid wound response gene promoter sequences enabled us to identify a novel DNA motif, designated the Rapid Stress Response Element. This motif is sufficient to confer a rapid response to both biotic and abiotic stresses in vivo, thereby confirming the functional involvement of this motif in the primary transcriptional stress response. The genes we identified may represent initial components of the general stress-response network and may be useful in engineering multi-stress tolerant plants.
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Affiliation(s)
- Justin W Walley
- Section of Plant Biology, University of California Davis, Davis, California, United States of America
| | - Sean Coughlan
- Agilent Technologies, Wilmington, Delaware, United States of America
| | - Matthew E Hudson
- Department of Crop Sciences, University Of Illinois, Urbana, Illinois, United States of America
| | - Michael F Covington
- Section of Plant Biology, University of California Davis, Davis, California, United States of America
| | - Roy Kaspi
- Section of Plant Biology, University of California Davis, Davis, California, United States of America
| | - Gopalan Banu
- Genomic Medicine, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Stacey L Harmer
- Section of Plant Biology, University of California Davis, Davis, California, United States of America
| | - Katayoon Dehesh
- Section of Plant Biology, University of California Davis, Davis, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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