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Zhao S, Cui Z, Zhang G, Gong Y, Su L. MGPPI: multiscale graph neural networks for explainable protein-protein interaction prediction. Front Genet 2024; 15:1440448. [PMID: 39076171 PMCID: PMC11284081 DOI: 10.3389/fgene.2024.1440448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 06/24/2024] [Indexed: 07/31/2024] Open
Abstract
Protein-Protein Interactions (PPIs) involves in various biological processes, which are of significant importance in cancer diagnosis and drug development. Computational based PPI prediction methods are more preferred due to their low cost and high accuracy. However, existing protein structure based methods are insufficient in the extraction of protein structural information. Furthermore, most methods are less interpretable, which hinder their practical application in the biomedical field. In this paper, we propose MGPPI, which is a Multiscale graph convolutional neural network model for PPI prediction. By incorporating multiscale module into the Graph Neural Network (GNN) and constructing multi convolutional layers, MGPPI can effectively capture both local and global protein structure information. For model interpretability, we introduce a novel visual explanation method named Gradient Weighted interaction Activation Mapping (Grad-WAM), which can highlight key binding residue sites. We evaluate the performance of MGPPI by comparing with state-of-the-arts methods on various datasets. Results shows that MGPPI outperforms other methods significantly and exhibits strong generalization capabilities on the multi-species dataset. As a practical case study, we predicted the binding affinity between the spike (S) protein of SARS-COV-2 and the human ACE2 receptor protein, and successfully identified key binding sites with known binding functions. Key binding sites mutation in PPIs can affect cancer patient survival statues. Therefore, we further verified Grad-WAM highlighted residue sites in separating patients survival groups in several different cancer type datasets. According to our results, some of the highlighted residues can be used as biomarkers in predicting patients survival probability. All these results together demonstrate the high accuracy and practical application value of MGPPI. Our method not only addresses the limitations of existing approaches but also can assists researchers in identifying crucial drug targets and help guide personalized cancer treatment.
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Affiliation(s)
| | | | | | | | - Lingtao Su
- College of Computer Science and Engineering, Shandong University of Science and Technology, Qingdao, China
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2
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Sun F, Deng Y, Ma X, Liu Y, Zhao L, Yu S, Zhang L. Structure-based prediction of protein-protein interaction network in rice. Genet Mol Biol 2024; 47:e20230068. [PMID: 38314883 PMCID: PMC10849033 DOI: 10.1590/1678-4685-gmb-2023-0068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 10/02/2023] [Indexed: 02/07/2024] Open
Abstract
Comprehensive protein-protein interaction (PPI) maps are critical for understanding the functional organization of the proteome, but challenging to produce experimentally. Here, we developed a computational method for predicting PPIs based on protein docking. Evaluation of performance on benchmark sets demonstrated the ability of the docking-based method to accurately identify PPIs using predicted protein structures. By employing the docking-based method, we constructed a structurally resolved PPI network consisting of 24,653 interactions between 2,131 proteins, which greatly extends the current knowledge on the rice protein-protein interactome. Moreover, we mapped the trait-associated single nucleotide polymorphisms (SNPs) to the structural interactome, and computationally identified 14 SNPs that had significant consequences on PPI network. The protein structural interactome map provided a resource to facilitate functional investigation of PPI-perturbing alleles associated with agronomically important traits in rice.
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Affiliation(s)
- Fangnan Sun
- Shanghai Jiao Tong University, School of Agriculture and Biology, Department of Plant Science, Shanghai, China
| | - Yaxin Deng
- Shanghai Jiao Tong University, School of Agriculture and Biology, Department of Plant Science, Shanghai, China
| | - Xiaosong Ma
- Shanghai Academy of Agricultural Sciences, Shanghai Agrobiological Gene Center, Shanghai, China
| | - Yuan Liu
- Shanghai Jiao Tong University, School of Agriculture and Biology, Department of Plant Science, Shanghai, China
| | - Lingxia Zhao
- Shanghai Jiao Tong University, School of Agriculture and Biology, Department of Plant Science, Shanghai, China
| | - Shunwu Yu
- Shanghai Academy of Agricultural Sciences, Shanghai Agrobiological Gene Center, Shanghai, China
| | - Lida Zhang
- Shanghai Jiao Tong University, School of Agriculture and Biology, Department of Plant Science, Shanghai, China
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3
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Choi J. Narrow funnel-like interaction energy distribution is an indicator of specific protein interaction partner. iScience 2023; 26:106911. [PMID: 37305691 PMCID: PMC10250834 DOI: 10.1016/j.isci.2023.106911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 04/28/2023] [Accepted: 05/12/2023] [Indexed: 06/13/2023] Open
Abstract
Protein interaction networks underlie countless biological mechanisms. However, most protein interaction predictions are based on biological evidence that are biased to well-known protein interaction or physical evidence that exhibits low accuracy for weak interactions and requires high computational power. In this study, a novel method has been suggested to predict protein interaction partners by investigating narrow funnel-like interaction energy distribution. In this study, it was demonstrated that various protein interactions including kinases and E3 ubiquitin ligases have narrow funnel-like interaction energy distribution. To analyze protein interaction distribution, modified scores of iRMS and TM-score are introduced. Then, using these scores, algorithm and deep learning model for prediction of protein interaction partner and substrate of kinase and E3 ubiquitin ligase were developed. The prediction accuracy was similar to or even better than that of yeast two-hybrid screening. Ultimately, this knowledge-free protein interaction prediction method will broaden our understanding of protein interaction networks.
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Affiliation(s)
- Juyoung Choi
- Department of Life Science, Sogang University, Seoul 04017, South Korea
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4
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Zheng J, Yang X, Huang Y, Yang S, Wuchty S, Zhang Z. Deep learning-assisted prediction of protein-protein interactions in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:984-994. [PMID: 36919205 DOI: 10.1111/tpj.16188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/20/2023] [Accepted: 03/09/2023] [Indexed: 05/27/2023]
Abstract
Currently, the experimentally identified interactome of Arabidopsis (Arabidopsis thaliana) is still far from complete, suggesting that computational prediction methods can complement experimental techniques. Motivated by the prosperity and success of deep learning algorithms and natural language processing techniques, we introduce an integrative deep learning framework, DeepAraPPI, allowing us to predict protein-protein interactions (PPIs) of Arabidopsis utilizing sequence, domain and Gene Ontology (GO) information. Our current DeepAraPPI comprises: (i) a word2vec encoding-based Siamese recurrent convolutional neural network (RCNN) model; (ii) a Domain2vec encoding-based multiple-layer perceptron (MLP) model; and (iii) a GO2vec encoding-based MLP model. Finally, DeepAraPPI combines the prediction results of the three individual predictors through a logistic regression model. Compiling high-quality positive and negative training and test samples by applying strict filtering strategies, DeepAraPPI shows superior performance compared with existing state-of-the-art Arabidopsis PPI prediction methods. DeepAraPPI also provides better cross-species predictive ability in rice (Oryza sativa) than traditional machine learning methods, although the overall performance in cross-species prediction remains to be improved. DeepAraPPI is freely accessible at http://zzdlab.com/deeparappi/. In the meantime, we have also made the source code and data sets of DeepAraPPI available at https://github.com/zjy1125/DeepAraPPI.
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Affiliation(s)
- Jingyan Zheng
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiaodi Yang
- Department of Hematology, Peking University First Hospital, Beijing, 100034, China
| | - Yan Huang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Shiping Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Stefan Wuchty
- Department of Computer Science, University of Miami, Miami, FL, 33146, USA
- Department of Biology, University of Miami, Miami, FL, 33146, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, 33136, USA
- Institute of Data Science and Computing, University of Miami, Miami, FL, 33146, USA
| | - Ziding Zhang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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5
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Mostaffa NH, Suhaimi AH, Al-Idrus A. Interactomics in plant defence: progress and opportunities. Mol Biol Rep 2023; 50:4605-4618. [PMID: 36920596 DOI: 10.1007/s11033-023-08345-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/15/2023] [Indexed: 03/16/2023]
Abstract
Interactomics is a branch of systems biology that deals with the study of protein-protein interactions and how these interactions influence phenotypes. Identifying the interactomes involved during host-pathogen interaction events may bring us a step closer to deciphering the molecular mechanisms underlying plant defence. Here, we conducted a systematic review of plant interactomics studies over the last two decades and found that while a substantial progress has been made in the field, plant-pathogen interactomics remains a less-travelled route. As an effort to facilitate the progress in this field, we provide here a comprehensive research pipeline for an in planta plant-pathogen interactomics study that encompasses the in silico prediction step to the validation step, unconfined to model plants. We also highlight four challenges in plant-pathogen interactomics with plausible solution(s) for each.
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Affiliation(s)
- Nur Hikmah Mostaffa
- Programme of Genetics, Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Ahmad Husaini Suhaimi
- Programme of Genetics, Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Aisyafaznim Al-Idrus
- Programme of Genetics, Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
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6
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Kim TW, Park CH, Hsu CC, Kim YW, Ko YW, Zhang Z, Zhu JY, Hsiao YC, Branon T, Kaasik K, Saldivar E, Li K, Pasha A, Provart NJ, Burlingame AL, Xu SL, Ting AY, Wang ZY. Mapping the signaling network of BIN2 kinase using TurboID-mediated biotin labeling and phosphoproteomics. THE PLANT CELL 2023; 35:975-993. [PMID: 36660928 PMCID: PMC10015162 DOI: 10.1093/plcell/koad013] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 11/29/2022] [Accepted: 01/13/2022] [Indexed: 05/27/2023]
Abstract
Elucidating enzyme-substrate relationships in posttranslational modification (PTM) networks is crucial for understanding signal transduction pathways but is technically difficult because enzyme-substrate interactions tend to be transient. Here, we demonstrate that TurboID-based proximity labeling (TbPL) effectively and specifically captures the substrates of kinases and phosphatases. TbPL-mass spectrometry (TbPL-MS) identified over 400 proximal proteins of Arabidopsis thaliana BRASSINOSTEROID-INSENSITIVE2 (BIN2), a member of the GLYCOGEN SYNTHASE KINASE 3 (GSK3) family that integrates signaling pathways controlling diverse developmental and acclimation processes. A large portion of the BIN2-proximal proteins showed BIN2-dependent phosphorylation in vivo or in vitro, suggesting that these are BIN2 substrates. Protein-protein interaction network analysis showed that the BIN2-proximal proteins include interactors of BIN2 substrates, revealing a high level of interactions among the BIN2-proximal proteins. Our proteomic analysis establishes the BIN2 signaling network and uncovers BIN2 functions in regulating key cellular processes such as transcription, RNA processing, translation initiation, vesicle trafficking, and cytoskeleton organization. We further discovered significant overlap between the GSK3 phosphorylome and the O-GlcNAcylome, suggesting an evolutionarily ancient relationship between GSK3 and the nutrient-sensing O-glycosylation pathway. Our work presents a powerful method for mapping PTM networks, a large dataset of GSK3 kinase substrates, and important insights into the signaling network that controls key cellular functions underlying plant growth and acclimation.
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Affiliation(s)
- Tae-Wuk Kim
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
- Department of Life Science, Hanyang University, Seoul 04763, South Korea
- Research Institute for Convergence of Basic Science, Hanyang University, Seoul 04763, South Korea
| | - Chan Ho Park
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
| | - Chuan-Chih Hsu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yeong-Woo Kim
- Department of Life Science, Hanyang University, Seoul 04763, South Korea
| | - Yeong-Woo Ko
- Department of Life Science, Hanyang University, Seoul 04763, South Korea
| | - Zhenzhen Zhang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
| | - Jia-Ying Zhu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
| | - Yu-Chun Hsiao
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
| | - Tess Branon
- Departments of Genetics, Biology, and Chemistry, Stanford University, Stanford, California 94305, USA
- Department of Biology, Stanford University, Stanford, California 94305, USA
- Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Krista Kaasik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, USA
| | - Evan Saldivar
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Kevin Li
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
| | - Asher Pasha
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Nicholas J Provart
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, USA
| | - Shou-Ling Xu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
| | - Alice Y Ting
- Departments of Genetics, Biology, and Chemistry, Stanford University, Stanford, California 94305, USA
- Department of Biology, Stanford University, Stanford, California 94305, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Zhi-Yong Wang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
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7
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Vandepoele K, Kaufmann K. Characterization of Gene Regulatory Networks in Plants Using New Methods and Data Types. Methods Mol Biol 2023; 2698:1-11. [PMID: 37682465 DOI: 10.1007/978-1-0716-3354-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
A major question in plant biology is to understand how plant growth, development, and environmental responses are controlled and coordinated by the activities of regulatory factors. Gene regulatory network (GRN) analyses require integrated approaches that combine experimental approaches with computational analyses. A wide range of experimental approaches and tools are now available, such as targeted perturbation of gene activities, quantitative and cell-type specific measurements of dynamic gene activities, and systematic analysis of the molecular 'hard-wiring' of the systems. At the computational level, different tools and databases are available to study regulatory sequences, including intuitive visualizations to explore data-driven gene regulatory networks in different plant species. Furthermore, advanced data integration approaches have recently been developed to efficiently leverage complementary regulatory data types and learn context-specific networks.
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Affiliation(s)
- Klaas Vandepoele
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium.
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium.
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.
| | - Kerstin Kaufmann
- Institute of Biology, Humboldt-Universitaet zu Berlin, Berlin, Germany
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8
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Lau V, Provart NJ. AGENT for Exploring and Analyzing Gene Regulatory Networks from Arabidopsis. Methods Mol Biol 2023; 2698:351-360. [PMID: 37682484 DOI: 10.1007/978-1-0716-3354-0_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Gene regulatory networks (GRNs) are important for determining how an organism develops and how it responds to external stimuli. In the case of Arabidopsis thaliana, several GRNs have been identified covering many important biological processes. We present AGENT, the Arabidopsis GEne Network Tool, for exploring and analyzing published GRNs. Using tools in AGENT, regulatory motifs such as feed-forward loops can be easily identified. Nodes with high centrality-and hence importance-can likewise be identified. Gene expression data can also be overlaid onto GRNs to help discover subnetworks acting in specific tissues or under certain conditions.
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Affiliation(s)
- Vincent Lau
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada.
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9
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Gouesbet G. Deciphering Macromolecular Interactions Involved in Abiotic Stress Signaling: A Review of Bioinformatics Analysis. Methods Mol Biol 2023; 2642:257-294. [PMID: 36944884 DOI: 10.1007/978-1-0716-3044-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Plant functioning and responses to abiotic stresses largely involve regulations at the transcriptomic level via complex interactions of signal molecules, signaling cascades, and regulators. Nevertheless, all the signaling networks involved in responses to abiotic stresses have not yet been fully established. The in-depth analysis of transcriptomes in stressed plants has become a relevant state-of-the-art methodology to study these regulations and signaling pathways that allow plants to cope with or attempt to survive abiotic stresses. The plant science and molecular biology community has developed databases about genes, proteins, protein-protein interactions, protein-DNA interactions and ontologies, which are valuable sources of knowledge for deciphering such regulatory and signaling networks. The use of these data and the development of bioinformatics tools help to make sense of transcriptomic data in specific contexts, such as that of abiotic stress signaling, using functional biological approaches. The aim of this chapter is to present and assess some of the essential online tools and resources that will allow novices in bioinformatics to decipher transcriptomic data in order to characterize the cellular processes and functions involved in abiotic stress responses and signaling. The analysis of case studies further describes how these tools can be used to conceive signaling networks on the basis of transcriptomic data. In these case studies, particular attention was paid to the characterization of abiotic stress responses and signaling related to chemical and xenobiotic stressors.
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Affiliation(s)
- Gwenola Gouesbet
- University of Rennes, CNRS, ECOBIO [(Ecosystèmes, Biodiversité, Evolution)] - UMR 6553, Rennes, France.
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10
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Smalley S, Hellmann H. Review: Exploring possible approaches using ubiquitylation and sumoylation pathways in modifying plant stress tolerance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 319:111275. [PMID: 35487671 DOI: 10.1016/j.plantsci.2022.111275] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
Ubiquitin and similar proteins, such as SUMO, are utilized by plants to modify target proteins to rapidly change their stability and activity in cells. This review will provide an overview of these crucial protein interactions with a focus on ubiquitylation and sumoylation in plants and how they contribute to stress tolerance. The work will also explore possibilities to use these highly conserved pathways for novel approaches to generate more robust crop plants better fit to cope with abiotic and biotic stress situations.
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Affiliation(s)
- Samuel Smalley
- Washington State University, Pullman, WA 99164, United States
| | - Hanjo Hellmann
- Washington State University, Pullman, WA 99164, United States.
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11
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Safder I, Shao G, Sheng Z, Hu P, Tang S. Genome-wide identification studies - A primer to explore new genes in plant species. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:9-22. [PMID: 34558163 DOI: 10.1111/plb.13340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
Genome data have accumulated rapidly in recent years, doubling roughly after every 6 months due to the influx of next-generation sequencing technologies. A plethora of plant genomes are available in comprehensive public databases. This easy access to data provides an opportunity to explore genome datasets and recruit new genes in various plant species not possible a decade ago. In the past few years, many gene families have been published using these public datasets. These genome-wide studies identify and characterize gene members, gene structures, evolutionary relationships, expression patterns, protein interactions and gene ontologies, and predict putative gene functions using various computational tools. Such studies provide meaningful information and an initial framework for further functional elucidation. This review provides a concise layout of approaches used in these gene family studies and demonstrates an outline for employing various plant genome datasets in future studies.
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Affiliation(s)
- I Safder
- State Key Laboratory of Rice Biology and China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
| | - G Shao
- State Key Laboratory of Rice Biology and China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
| | - Z Sheng
- State Key Laboratory of Rice Biology and China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
| | - P Hu
- State Key Laboratory of Rice Biology and China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
| | - S Tang
- State Key Laboratory of Rice Biology and China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China
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12
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Cantó-Pastor A, Mason GA, Brady SM, Provart NJ. Arabidopsis bioinformatics: tools and strategies. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1585-1596. [PMID: 34695270 DOI: 10.1111/tpj.15547] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/01/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
The sequencing of the Arabidopsis thaliana genome 21 years ago ushered in the genomics era for plant research. Since then, an incredible variety of bioinformatic tools permit easy access to large repositories of genomic, transcriptomic, proteomic, epigenomic and other '-omic' data. In this review, we cover some more recent tools (and highlight the 'classics') for exploring such data in order to help formulate quality, testable hypotheses, often without having to generate new experimental data. We cover tools for examining gene expression and co-expression patterns, undertaking promoter analyses and gene set enrichment analyses, and exploring protein-protein and protein-DNA interactions. We will touch on tools that integrate different data sets at the end of the article.
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Affiliation(s)
- Alex Cantó-Pastor
- Department of Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - G Alex Mason
- Department of Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
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13
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Navarro C, Mateo-Elizalde C, Mohan TC, Sánchez-Bermejo E, Urrutia O, Fernández-Muñiz MN, García-Mina JM, Muñoz R, Paz-Ares J, Castrillo G, Leyva A. Arsenite provides a selective signal that coordinates arsenate uptake and detoxification through the regulation of PHR1 stability in Arabidopsis. MOLECULAR PLANT 2021; 14:1489-1507. [PMID: 34048950 DOI: 10.1016/j.molp.2021.05.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 04/30/2021] [Accepted: 05/24/2021] [Indexed: 06/12/2023]
Abstract
In nature, plants acquire nutrients from soils to sustain growth, and at the same time, they need to avoid the uptake of toxic compounds and/or possess tolerance systems to cope with them. This is particularly challenging when the toxic compound and the nutrient are chemically similar, as in the case of phosphate and arsenate. In this study, we demonstrated that regulatory elements of the phosphate starvation response (PSR) coordinate the arsenate detoxification machinery in the cell. We showed that arsenate repression of the phosphate transporter PHT1;1 is associated with the degradation of the PSR master regulator PHR1. Once arsenic is sequestered into the vacuole, PHR1 stability is restored and PHT1;1 expression is recovered. Furthermore, we identified an arsenite responsive SKP1-like protein and a PHR1 interactor F-box (PHIF1) as constituents of the SCF complex responsible for PHR1 degradation.We found that arsenite, the form to which arsenate is reduced for compartmentalization in vacuoles, represses PHT1;1 expression, providing a highly selective signal versus phosphate to control PHT1;1 expression in response to arsenate. Collectively, our results provide molecular insights into a sensing mechanism that regulates arsenate/phosphate uptake depending on the plant's detoxification capacity.
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Affiliation(s)
- Cristina Navarro
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
| | - Cristian Mateo-Elizalde
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
| | - Thotegowdanapalya C Mohan
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
| | - Eduardo Sánchez-Bermejo
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
| | - Oscar Urrutia
- Department of Environmental Biology, Sciences School, University of Navarra, Pamplona 31008, Spain
| | - María Nieves Fernández-Muñiz
- Department of Analytical Chemistry, School of Chemical Sciences, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - José M García-Mina
- Department of Environmental Biology, Sciences School, University of Navarra, Pamplona 31008, Spain
| | - Riansares Muñoz
- Department of Analytical Chemistry, School of Chemical Sciences, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Javier Paz-Ares
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
| | - Gabriel Castrillo
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain.
| | - Antonio Leyva
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain.
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14
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Kerbler SM, Natale R, Fernie AR, Zhang Y. From Affinity to Proximity Techniques to Investigate Protein Complexes in Plants. Int J Mol Sci 2021; 22:ijms22137101. [PMID: 34281155 PMCID: PMC8267905 DOI: 10.3390/ijms22137101] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/22/2021] [Accepted: 06/28/2021] [Indexed: 02/02/2023] Open
Abstract
The study of protein–protein interactions (PPIs) is fundamental in understanding the unique role of proteins within cells and their contribution to complex biological systems. While the toolkit to study PPIs has grown immensely in mammalian and unicellular eukaryote systems over recent years, application of these techniques in plants remains under-utilized. Affinity purification coupled to mass spectrometry (AP-MS) and proximity labeling coupled to mass spectrometry (PL-MS) are two powerful techniques that have significantly enhanced our understanding of PPIs. Relying on the specific binding properties of a protein to an immobilized ligand, AP is a fast, sensitive and targeted approach used to detect interactions between bait (protein of interest) and prey (interacting partners) under near-physiological conditions. Similarly, PL, which utilizes the close proximity of proteins to identify potential interacting partners, has the ability to detect transient or hydrophobic interactions under native conditions. Combined, these techniques have the potential to reveal an unprecedented spatial and temporal protein interaction network that better understands biological processes relevant to many fields of interest. In this review, we summarize the advantages and disadvantages of two increasingly common PPI determination techniques: AP-MS and PL-MS and discuss their important application to plant systems.
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Affiliation(s)
- Sandra M. Kerbler
- Theodor-Echtermeyer-Weg 1, Leibniz-Institut für Gemüse- und Zierpflanzenbau, 14979 Groβbeeren, Germany;
| | - Roberto Natale
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; (R.N.); (A.R.F.)
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; (R.N.); (A.R.F.)
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Youjun Zhang
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; (R.N.); (A.R.F.)
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Correspondence:
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15
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Provart NJ, Brady SM, Parry G, Schmitz RJ, Queitsch C, Bonetta D, Waese J, Schneeberger K, Loraine AE. Anno genominis XX: 20 years of Arabidopsis genomics. THE PLANT CELL 2021; 33:832-845. [PMID: 33793861 PMCID: PMC8226293 DOI: 10.1093/plcell/koaa038] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/09/2020] [Indexed: 05/04/2023]
Abstract
Twenty years ago, the Arabidopsis thaliana genome sequence was published. This was an important moment as it was the first sequenced plant genome and explicitly brought plant science into the genomics era. At the time, this was not only an outstanding technological achievement, but it was characterized by a superb global collaboration. The Arabidopsis genome was the seed for plant genomic research. Here, we review the development of numerous resources based on the genome that have enabled discoveries across plant species, which has enhanced our understanding of how plants function and interact with their environments.
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Affiliation(s)
- Nicholas J Provart
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, California, 95616, USA
| | - Geraint Parry
- GARNet, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Georgia, 30602, USA
| | - Christine Queitsch
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington, 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, 98195, USA
| | - Dario Bonetta
- Faculty of Science, Ontario Tech University, Oshawa, Ontario, L1G 0C5, Canada
| | - Jamie Waese
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, D-50829, Cologne, Germany
- Faculty of Biology, LMU Munich, 82152 Munich, Germany
| | - Ann E Loraine
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
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16
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Khouider S, Borges F, LeBlanc C, Ungru A, Schnittger A, Martienssen R, Colot V, Bouyer D. Male fertility in Arabidopsis requires active DNA demethylation of genes that control pollen tube function. Nat Commun 2021; 12:410. [PMID: 33462227 PMCID: PMC7813888 DOI: 10.1038/s41467-020-20606-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 12/11/2020] [Indexed: 12/31/2022] Open
Abstract
Active DNA demethylation is required for sexual reproduction in plants but the molecular determinants underlying this epigenetic control are not known. Here, we show in Arabidopsis thaliana that the DNA glycosylases DEMETER (DME) and REPRESSOR OF SILENCING 1 (ROS1) act semi-redundantly in the vegetative cell of pollen to demethylate DNA and ensure proper pollen tube progression. Moreover, we identify six pollen-specific genes with increased DNA methylation as well as reduced expression in dme and dme;ros1. We further show that for four of these genes, reinstalling their expression individually in mutant pollen is sufficient to improve male fertility. Our findings demonstrate an essential role of active DNA demethylation in regulating genes involved in pollen function.
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Affiliation(s)
- Souraya Khouider
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University, 75005, Paris, France
| | - Filipe Borges
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA.,Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Chantal LeBlanc
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA.,Faculty of Arts and Sciences, Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06511, USA
| | - Alexander Ungru
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Arp Schnittger
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.,Institut de Biologie Moleculaire des Plantes (IBMP), CNRS, University Strasbourg, 67084, Strasbourg, France.,University Hamburg, 22609, Hamburg, Germany
| | - Robert Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA
| | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University, 75005, Paris, France.
| | - Daniel Bouyer
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University, 75005, Paris, France. .,Institut de Biologie Moleculaire des Plantes (IBMP), CNRS, University Strasbourg, 67084, Strasbourg, France. .,Laboratoire Reproduction et Développement des Plantes (RDP), UnivLyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon1, CNRS, INRAE, 69342, Lyon, France.
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17
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Zhang Y, Fernie AR. Metabolons, enzyme-enzyme assemblies that mediate substrate channeling, and their roles in plant metabolism. PLANT COMMUNICATIONS 2021; 2:100081. [PMID: 33511342 PMCID: PMC7816073 DOI: 10.1016/j.xplc.2020.100081] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 05/05/2023]
Abstract
Metabolons are transient multi-protein complexes of sequential enzymes that mediate substrate channeling. They differ from multi-enzyme complexes in that they are dynamic, rather than permanent, and as such have considerably lower dissociation constants. Despite the fact that a huge number of metabolons have been suggested to exist in plants, most of these claims are erroneous as only a handful of these have been proven to channel metabolites. We believe that physical protein-protein interactions between consecutive enzymes of a pathway should rather be called enzyme-enzyme assemblies. In this review, we describe how metabolons are generally assembled by transient interactions and held together by both structural elements and non-covalent interactions. Experimental evidence for their existence comes from protein-protein interaction studies, which indicate that the enzymes physically interact, and direct substrate channeling measurements, which indicate that they functionally interact. Unfortunately, advances in cell biology and proteomics have far outstripped those in classical enzymology and flux measurements, rendering most reports reliant purely on interactome studies. Recent developments in co-fractionation mass spectrometry will likely further exacerbate this bias. Given this, only dynamic enzyme-enzyme assemblies in which both physical and functional interactions have been demonstrated should be termed metabolons. We discuss the level of evidence for the manifold plant pathways that have been postulated to contain metabolons and then list examples in both primary and secondary metabolism for which strong evidence has been provided to support these claims. In doing so, we pay particular attention to experimental and mathematical approaches to study metabolons as well as complexities that arise in attempting to follow them. Finally, we discuss perspectives for improving our understanding of these fascinating but enigmatic interactions.
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Affiliation(s)
- Youjun Zhang
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R. Fernie
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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18
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Oughtred R, Rust J, Chang C, Breitkreutz B, Stark C, Willems A, Boucher L, Leung G, Kolas N, Zhang F, Dolma S, Coulombe‐Huntington J, Chatr‐aryamontri A, Dolinski K, Tyers M. The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions. Protein Sci 2021; 30:187-200. [PMID: 33070389 PMCID: PMC7737760 DOI: 10.1002/pro.3978] [Citation(s) in RCA: 673] [Impact Index Per Article: 224.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/09/2020] [Accepted: 10/13/2020] [Indexed: 02/06/2023]
Abstract
The BioGRID (Biological General Repository for Interaction Datasets, thebiogrid.org) is an open-access database resource that houses manually curated protein and genetic interactions from multiple species including yeast, worm, fly, mouse, and human. The ~1.93 million curated interactions in BioGRID can be used to build complex networks to facilitate biomedical discoveries, particularly as related to human health and disease. All BioGRID content is curated from primary experimental evidence in the biomedical literature, and includes both focused low-throughput studies and large high-throughput datasets. BioGRID also captures protein post-translational modifications and protein or gene interactions with bioactive small molecules including many known drugs. A built-in network visualization tool combines all annotations and allows users to generate network graphs of protein, genetic and chemical interactions. In addition to general curation across species, BioGRID undertakes themed curation projects in specific aspects of cellular regulation, for example the ubiquitin-proteasome system, as well as specific disease areas, such as for the SARS-CoV-2 virus that causes COVID-19 severe acute respiratory syndrome. A recent extension of BioGRID, named the Open Repository of CRISPR Screens (ORCS, orcs.thebiogrid.org), captures single mutant phenotypes and genetic interactions from published high throughput genome-wide CRISPR/Cas9-based genetic screens. BioGRID-ORCS contains datasets for over 1,042 CRISPR screens carried out to date in human, mouse and fly cell lines. The biomedical research community can freely access all BioGRID data through the web interface, standardized file downloads, or via model organism databases and partner meta-databases.
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Affiliation(s)
- Rose Oughtred
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNew JerseyUSA
| | - Jennifer Rust
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNew JerseyUSA
| | - Christie Chang
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNew JerseyUSA
| | | | - Chris Stark
- The Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoOntarioCanada
| | - Andrew Willems
- The Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoOntarioCanada
| | - Lorrie Boucher
- The Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoOntarioCanada
| | - Genie Leung
- The Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoOntarioCanada
| | - Nadine Kolas
- The Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoOntarioCanada
| | - Frederick Zhang
- Arthur and Sonia Labatt Brain Tumor Research Center and Developmental and Stem Cell BiologyThe Hospital for Sick ChildrenTorontoOntarioCanada
| | - Sonam Dolma
- Arthur and Sonia Labatt Brain Tumor Research Center and Developmental and Stem Cell BiologyThe Hospital for Sick ChildrenTorontoOntarioCanada
| | | | | | - Kara Dolinski
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNew JerseyUSA
| | - Mike Tyers
- The Lunenfeld‐Tanenbaum Research InstituteMount Sinai HospitalTorontoOntarioCanada
- Institute for Research in Immunology and CancerUniversité de MontréalQuebecCanada
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19
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Abstract
Bioinformatic tools are now an everyday part of a plant researcher's collection of protocols. They allow almost instantaneous access to large data sets encompassing genomes, transcriptomes, proteomes, epigenomes, and other "-omes," which are now being generated with increasing speed and decreasing cost. With the appropriate queries, such tools can generate quality hypotheses, sometimes without the need for new experimental data. In this chapter, we will investigate some of the tools used for examining gene expression and coexpression patterns, performing promoter analyses and functional classification enrichment for sets of genes, and exploring protein-protein and protein-DNA interactions in Arabidopsis. We will also cover additional tools that allow integration of data from several sources for improved hypothesis generation.
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Affiliation(s)
- G Alex Mason
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Alex Cantó-Pastor
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Nicholas J Provart
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada.
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20
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Mondal R, Das P. Data-mining bioinformatics: suggesting Arabidopsis thaliana L-type lectin receptor kinase IX.2 ( LecRK-IX.2) modulate metabolites and abiotic stress responses. PLANT SIGNALING & BEHAVIOR 2020; 15:1818031. [PMID: 32924779 PMCID: PMC7671074 DOI: 10.1080/15592324.2020.1818031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 05/31/2023]
Abstract
The central role of the Arabidopsis LecRK-IX.2 gene in response to biotic stress has been well established by an array of workers. So far, the role of LecRK-IX.2 in abiotic stresses has not been investigated systematically. Here, we have first investigated a comprehensive in silico survey to explore the regulation, expression pattern in responses to a wide range of abiotic stresses. The present study reveals that the LecRK-IX.2 promoter has numerous potential cis-regulatory elements (CREs) that are regulated by different stresses. AtGenExpress data elucidate that LecRK-IX.2 gene plays a potential role in responses to cold, osmotic, drought, salt, UV-B, heat, wound, and genotoxic compound. The expression profile of the co-expressed genes suggests that Arabidopsis LecRK-IX.2 gene might have a potential role in stress responses in a tissue-specific manner. Furthermore, a probable signal transduction mechanism has been described by using protein-protein interaction (PPI) dataset. Moreover, the present data-mining investigations have suggested that LecRK-IX.2 gene modulates cellular metabolites and abiotic stress responses.
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Affiliation(s)
- Raju Mondal
- Mulberry Tissue Culture Lab, Mulberry Division, Central Sericultural Germplasm Resources Centre (CSGRC), Hosur, India
| | - Poushali Das
- Taxonomy and Biosystematic Laboratory, Department of Botany, University of Calcutta, Kolkata, India
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21
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Ko DK, Brandizzi F. Network-based approaches for understanding gene regulation and function in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:302-317. [PMID: 32717108 PMCID: PMC8922287 DOI: 10.1111/tpj.14940] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 07/14/2020] [Indexed: 05/03/2023]
Abstract
Expression reprogramming directed by transcription factors is a primary gene regulation underlying most aspects of the biology of any organism. Our views of how gene regulation is coordinated are dramatically changing thanks to the advent and constant improvement of high-throughput profiling and transcriptional network inference methods: from activities of individual genes to functional interactions across genes. These technical and analytical advances can reveal the topology of transcriptional networks in which hundreds of genes are hierarchically regulated by multiple transcription factors at systems level. Here we review the state of the art of experimental and computational methods used in plant biology research to obtain large-scale datasets and model transcriptional networks. Examples of direct use of these network models and perspectives on their limitations and future directions are also discussed.
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Affiliation(s)
- Dae Kwan Ko
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI 48824, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI 48824, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
- For correspondence ()
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22
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Oña Chuquimarca S, Ayala-Ruano S, Goossens J, Pauwels L, Goossens A, Leon-Reyes A, Ángel Méndez M. The Molecular Basis of JAZ-MYC Coupling, a Protein-Protein Interface Essential for Plant Response to Stressors. FRONTIERS IN PLANT SCIENCE 2020; 11:1139. [PMID: 32973821 PMCID: PMC7468482 DOI: 10.3389/fpls.2020.01139] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/14/2020] [Indexed: 05/29/2023]
Abstract
The jasmonic acid (JA) signaling pathway is one of the primary mechanisms that allow plants to respond to a variety of biotic and abiotic stressors. Within this pathway, the JAZ repressor proteins and the basic helix-loop-helix (bHLH) transcription factor MYC3 play a critical role. JA is a volatile organic compound with an essential role in plant immunity. The increase in the concentration of JA leads to the decoupling of the JAZ repressor proteins and the bHLH transcription factor MYC3 causing the induction of genes of interest. The primary goal of this study was to identify the molecular basis of JAZ-MYC coupling. For this purpose, we modeled and validated 12 JAZ-MYC3 3D in silico structures and developed a molecular dynamics/machine learning pipeline to obtain two outcomes. First, we calculated the average free binding energy of JAZ-MYC3 complexes, which was predicted to be -10.94 +/-2.67 kJ/mol. Second, we predicted which ones should be the interface residues that make the predominant contribution to the free energy of binding (molecular hotspots). The predicted protein hotspots matched a conserved linear motif SL••FL•••R, which may have a crucial role during MYC3 recognition of JAZ proteins. As a proof of concept, we tested, both in silico and in vitro, the importance of this motif on PEAPOD (PPD) proteins, which also belong to the TIFY protein family, like the JAZ proteins, but cannot bind to MYC3. By mutating these proteins to match the SL••FL•••R motif, we could force PPDs to bind the MYC3 transcription factor. Taken together, modeling protein-protein interactions and using machine learning will help to find essential motifs and molecular mechanisms in the JA pathway.
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Affiliation(s)
- Samara Oña Chuquimarca
- Grupo de Química Computacional y Teórica, Departamento de Ingeniería Química, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Quito, Ecuador
- Instituto de Simulación Computacional (ISC-USFQ), Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Sebastián Ayala-Ruano
- Grupo de Química Computacional y Teórica, Departamento de Ingeniería Química, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Quito, Ecuador
- Instituto de Simulación Computacional (ISC-USFQ), Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Jonas Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Laurens Pauwels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Antonio Leon-Reyes
- Laboratorio de Biotecnología Agrícola y de Alimentos, Ingeniería en Agronomía, Colegio de Ciencias e Ingenierías, Universidad San Francisco de Quito, Campus Cumbayá, Quito, Ecuador
- Colegio de Ciencias Biológicas y Ambientales COCIBA, Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Quito, Ecuador
- Colegio de Ciencias Biológicas y Ambientales COCIBA, Instituto de Investigaciones Biológicas y Ambientales BIÓSFERA, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Quito, Ecuador
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Miguel Ángel Méndez
- Grupo de Química Computacional y Teórica, Departamento de Ingeniería Química, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Quito, Ecuador
- Instituto de Simulación Computacional (ISC-USFQ), Universidad San Francisco de Quito USFQ, Quito, Ecuador
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23
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Song MJ, Potter BI, Doyle JJ, Coate JE. Gene Balance Predicts Transcriptional Responses Immediately Following Ploidy Change in Arabidopsis thaliana. THE PLANT CELL 2020; 32:1434-1448. [PMID: 32184347 PMCID: PMC7203931 DOI: 10.1105/tpc.19.00832] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 02/18/2020] [Accepted: 03/14/2020] [Indexed: 05/22/2023]
Abstract
The gene balance hypothesis postulates that there is selection on gene copy number (gene dosage) to preserve the stoichiometric balance among interacting proteins. This presupposes that gene product abundance is governed by gene dosage and that gene dosage responses are consistent for interacting genes in a dosage-balance-sensitive network or complex. Gene dosage responses, however, have rarely been quantified, and the available data suggest that they are highly variable. We sequenced the transcriptomes of two synthetic autopolyploid accessions of Arabidopsis (Arabidopsis thaliana) and their diploid progenitors, as well as one natural tetraploid and its synthetic diploid produced via haploid induction, to estimate transcriptome size and dosage responses immediately following ploidy change. Similar to what has been observed in previous studies, overall transcriptome size does not exhibit a simple doubling in response to genome doubling, and individual gene dosage responses are highly variable in all three accessions, indicating that expression is not strictly coupled with gene dosage. Nonetheless, putatively dosage balance-sensitive gene groups (Gene Ontology terms, metabolic networks, gene families, and predicted interacting proteins) exhibit smaller and more coordinated dosage responses than do putatively dosage-insensitive gene groups, suggesting that constraints on dosage balance operate immediately following whole-genome duplication and that duplicate gene retention patterns are shaped by selection to preserve dosage balance.
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Affiliation(s)
- Michael J Song
- University and Jepson Herbaria and Department of Integrative Biology, University of California, Berkeley, California 94720
| | - Barney I Potter
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - Jeff J Doyle
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
| | - Jeremy E Coate
- Department of Biology, Reed College, Portland, Oregon 97202
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24
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Yang X, Yang S, Qi H, Wang T, Li H, Zhang Z. PlaPPISite: a comprehensive resource for plant protein-protein interaction sites. BMC PLANT BIOLOGY 2020; 20:61. [PMID: 32028878 PMCID: PMC7006421 DOI: 10.1186/s12870-020-2254-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 01/16/2020] [Indexed: 05/02/2023]
Abstract
BACKGROUND Protein-protein interactions (PPIs) play very important roles in diverse biological processes. Experimentally validated or predicted PPI data have become increasingly available in diverse plant species. To further explore the biological functions of PPIs, understanding the interaction details of plant PPIs (e.g., the 3D structural contexts of interaction sites) is necessary. By integrating bioinformatics algorithms, interaction details can be annotated at different levels and then compiled into user-friendly databases. In our previous study, we developed AraPPISite, which aimed to provide interaction site information for PPIs in the model plant Arabidopsis thaliana. Considering that the application of AraPPISite is limited to one species, it is very natural that AraPPISite should be evolved into a new database that can provide interaction details of PPIs in multiple plants. DESCRIPTION PlaPPISite (http://zzdlab.com/plappisite/index.php) is a comprehensive, high-coverage and interaction details-oriented database for 13 plant interactomes. In addition to collecting 121 experimentally verified structures of protein complexes, the complex structures of experimental/predicted PPIs in the 13 plants were also constructed, and the corresponding interaction sites were annotated. For the PPIs whose 3D structures could not be modelled, the associated domain-domain interactions (DDIs) and domain-motif interactions (DMIs) were inferred. To facilitate the reliability assessment of predicted PPIs, the source species of interolog templates, GO annotations, subcellular localizations and gene expression similarities are also provided. JavaScript packages were employed to visualize structures of protein complexes, protein interaction sites and protein interaction networks. We also developed an online tool for homology modelling and protein interaction site annotation of protein complexes. All data contained in PlaPPISite are also freely available on the Download page. CONCLUSION PlaPPISite provides the plant research community with an easy-to-use and comprehensive data resource for the search and analysis of protein interaction details from the 13 important plant species.
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Affiliation(s)
- Xiaodi Yang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193 China
| | - Shiping Yang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193 China
| | - Huan Qi
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193 China
| | - Tianpeng Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193 China
| | - Hong Li
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228 China
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193 China
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Streich J, Romero J, Gazolla JGFM, Kainer D, Cliff A, Prates ET, Brown JB, Khoury S, Tuskan GA, Garvin M, Jacobson D, Harfouche AL. Can exascale computing and explainable artificial intelligence applied to plant biology deliver on the United Nations sustainable development goals? Curr Opin Biotechnol 2020; 61:217-225. [DOI: 10.1016/j.copbio.2020.01.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 01/27/2020] [Accepted: 01/28/2020] [Indexed: 01/26/2023]
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Ran X, Zhao F, Wang Y, Liu J, Zhuang Y, Ye L, Qi M, Cheng J, Zhang Y. Plant Regulomics: a data-driven interface for retrieving upstream regulators from plant multi-omics data. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:237-248. [PMID: 31494994 DOI: 10.1111/tpj.14526] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/31/2019] [Accepted: 08/19/2019] [Indexed: 05/19/2023]
Abstract
High-throughput technology has become a powerful approach for routine plant research. Interpreting the biological significance of high-throughput data has largely focused on the functional characterization of a large gene list or genomic loci that involves the following two aspects: the functions of the genes or loci and how they are regulated as a whole, i.e. searching for the upstream regulators. Traditional platforms for functional annotation largely help resolving the first issue. Addressing the second issue is essential for a global understanding of the regulatory mechanism, but is more challenging, and requires additional high-throughput experimental evidence and a unified statistical framework for data-mining. The rapid accumulation of 'omics data provides a large amount of experimental data. We here present Plant Regulomics, an interface that integrates 19 925 transcriptomic and epigenomic data sets and diverse sources of functional evidence (58 112 terms and 695 414 protein-protein interactions) from six plant species along with the orthologous genes from 56 whole-genome sequenced plant species. All pair-wise transcriptomic comparisons with biological significance within the same study were performed, and all epigenomic data were processed to genomic loci targeted by various factors. These data were well organized to gene modules and loci lists, which were further implemented into the same statistical framework. For any input gene list or genomic loci, Plant Regulomics retrieves the upstream factors, treatments, and experimental/environmental conditions regulating the input from the integrated 'omics data. Additionally, multiple tools and an interactive visualization are available through a user-friendly web interface. Plant Regulomics is available at http://bioinfo.sibs.ac.cn/plant-regulomics.
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Affiliation(s)
- Xiaojuan Ran
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Fei Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuejun Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yili Zhuang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Luhuan Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Meifang Qi
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingfei Cheng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yijing Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
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Inference of plant gene regulatory networks using data-driven methods: A practical overview. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1863:194447. [PMID: 31678628 DOI: 10.1016/j.bbagrm.2019.194447] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 10/08/2019] [Accepted: 10/31/2019] [Indexed: 11/20/2022]
Abstract
Transcriptional regulation is a complex and dynamic process that plays a vital role in plant growth and development. A key component in the regulation of genes is transcription factors (TFs), which coordinate the transcriptional control of gene activity. A gene regulatory network (GRN) is a collection of regulatory interactions between TFs and their target genes. The accurate delineation of GRNs offers a significant contribution to our understanding about how plant cells are organized and function, and how individual genes are regulated in various conditions, organs or cell types. During the past decade, important progress has been made in the identification of GRNs using experimental and computational approaches. However, a detailed overview of available platforms supporting the analysis of GRNs in plants is missing. Here, we review current databases, platforms and tools that perform data-driven analyses of gene regulation in Arabidopsis. The platforms are categorized into two sections, 1) promoter motif analysis tools that use motif mapping approaches to find TF motifs in the regulatory sequences of genes of interest and 2) network analysis tools that identify potential regulators for a set of input genes using a range of data types in order to generate GRNs. We discuss the diverse datasets integrated and highlight the strengths and caveats of different platforms. Finally, we shed light on the limitations of the above approaches and discuss future perspectives, including the need for integrative approaches to unravel complex GRNs in plants.
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Cao FY, Khan M, Taniguchi M, Mirmiran A, Moeder W, Lumba S, Yoshioka K, Desveaux D. A host-pathogen interactome uncovers phytopathogenic strategies to manipulate plant ABA responses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:187-198. [PMID: 31148337 DOI: 10.1111/tpj.14425] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 04/05/2018] [Accepted: 05/22/2019] [Indexed: 05/21/2023]
Abstract
The phytopathogen Pseudomonas syringae delivers into host cells type III secreted effectors (T3SEs) that promote virulence. One virulence mechanism employed by T3SEs is to target hormone signaling pathways to perturb hormone homeostasis. The phytohormone abscisic acid (ABA) influences interactions between various phytopathogens and their plant hosts, and has been shown to be a target of P. syringae T3SEs. In order to provide insight into how T3SEs manipulate ABA responses, we generated an ABA-T3SE interactome network (ATIN) between P. syringae T3SEs and Arabidopsis proteins encoded by ABA-regulated genes. ATIN consists of 476 yeast-two-hybrid interactions between 97 Arabidopsis ABA-regulated proteins and 56 T3SEs from four pathovars of P. syringae. We demonstrate that T3SE interacting proteins are significantly enriched for proteins associated with transcription. In particular, the ETHYLENE RESPONSIVE FACTOR (ERF) family of transcription factors is highly represented. We show that ERF105 and ERF8 displayed a role in defense against P. syringae, supporting our overall observation that T3SEs of ATIN converge on proteins that influence plant immunity. In addition, we demonstrate that T3SEs that interact with a large number of ABA-regulated proteins can influence ABA responses. One of these T3SEs, HopF3Pph6 , inhibits the function of ERF8, which influences both ABA-responses and plant immunity. These results provide a potential mechanism for how HopF3Pph6 manipulates ABA-responses to promote P. syringae virulence, and also demonstrate the utility of ATIN as a resource to study the ABA-T3SE interface.
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Affiliation(s)
- Feng Y Cao
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St, Toronto, Ontario, M5S 3B2, Canada
| | - Madiha Khan
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St, Toronto, Ontario, M5S 3B2, Canada
| | - Masatoshi Taniguchi
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St, Toronto, Ontario, M5S 3B2, Canada
| | - Armand Mirmiran
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St, Toronto, Ontario, M5S 3B2, Canada
| | - Wolfgang Moeder
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St, Toronto, Ontario, M5S 3B2, Canada
| | - Shelley Lumba
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St, Toronto, Ontario, M5S 3B2, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
| | - Keiko Yoshioka
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St, Toronto, Ontario, M5S 3B2, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
| | - Darrell Desveaux
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St, Toronto, Ontario, M5S 3B2, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
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Cytological and Proteomic Analysis of Wheat Pollen Abortion Induced by Chemical Hybridization Agent. Int J Mol Sci 2019; 20:ijms20071615. [PMID: 30939734 PMCID: PMC6480110 DOI: 10.3390/ijms20071615] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/24/2019] [Accepted: 03/27/2019] [Indexed: 12/13/2022] Open
Abstract
In plants, pollen grain transfers the haploid male genetic material from anther to stigma, both between flowers (cross-pollination) and within the same flower (self-pollination). In order to better understand chemical hybridizing agent (CHA) SQ-1-induced pollen abortion in wheat, comparative cytological and proteomic analyses were conducted. Results indicated that pollen grains underwent serious structural injury, including cell division abnormality, nutritional deficiencies, pollen wall defect and pollen grain malformations in the CHA-SQ-1-treated plants, resulting in pollen abortion and male sterility. A total of 61 proteins showed statistically significant differences in abundance, among which 18 proteins were highly abundant and 43 proteins were less abundant in CHA-SQ-1 treated plants. 60 proteins were successfully identified using MALDI-TOF/TOF mass spectrometry. These proteins were found to be involved in pollen maturation and showed a change in the abundance of a battery of proteins involved in multiple biological processes, including pollen development, carbohydrate and energy metabolism, stress response, protein metabolism. Interactions between these proteins were predicted using bioinformatics analysis. Gene ontology and pathway analyses revealed that the majority of the identified proteins were involved in carbohydrate and energy metabolism. Accordingly, a protein-protein interaction network involving in pollen abortion was proposed. These results provide information for the molecular events underlying CHA-SQ-1-induced pollen abortion and may serve as an additional guide for practical hybrid breeding.
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