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Esmaili F, Pourmirzaei M, Ramazi S, Shojaeilangari S, Yavari E. A Review of Machine Learning and Algorithmic Methods for Protein Phosphorylation Site Prediction. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:1266-1285. [PMID: 37863385 PMCID: PMC11082408 DOI: 10.1016/j.gpb.2023.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 01/16/2023] [Accepted: 03/23/2023] [Indexed: 10/22/2023]
Abstract
Post-translational modifications (PTMs) have key roles in extending the functional diversity of proteins and, as a result, regulating diverse cellular processes in prokaryotic and eukaryotic organisms. Phosphorylation modification is a vital PTM that occurs in most proteins and plays a significant role in many biological processes. Disorders in the phosphorylation process lead to multiple diseases, including neurological disorders and cancers. The purpose of this review is to organize this body of knowledge associated with phosphorylation site (p-site) prediction to facilitate future research in this field. At first, we comprehensively review all related databases and introduce all steps regarding dataset creation, data preprocessing, and method evaluation in p-site prediction. Next, we investigate p-site prediction methods, which are divided into two computational groups: algorithmic and machine learning (ML). Additionally, it is shown that there are basically two main approaches for p-site prediction by ML: conventional and end-to-end deep learning methods, both of which are given an overview. Moreover, this review introduces the most important feature extraction techniques, which have mostly been used in p-site prediction. Finally, we create three test sets from new proteins related to the released version of the database of protein post-translational modifications (dbPTM) in 2022 based on general and human species. Evaluating online p-site prediction tools on newly added proteins introduced in the dbPTM 2022 release, distinct from those in the dbPTM 2019 release, reveals their limitations. In other words, the actual performance of these online p-site prediction tools on unseen proteins is notably lower than the results reported in their respective research papers.
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Affiliation(s)
- Farzaneh Esmaili
- Department of Information Technology, Tarbiat Modares University, Tehran 14115-111, Iran
| | - Mahdi Pourmirzaei
- Department of Information Technology, Tarbiat Modares University, Tehran 14115-111, Iran
| | - Shahin Ramazi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-111, Iran.
| | - Seyedehsamaneh Shojaeilangari
- Biomedical Engineering Group, Department of Electrical Engineering and Information Technology, Iranian Research Organization for Science and Technology (IROST), Tehran 33535-111, Iran
| | - Elham Yavari
- Department of Information Technology, Tarbiat Modares University, Tehran 14115-111, Iran
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2
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Pasquier C, Robichon A. Evolutionary Divergence of Phosphorylation to Regulate Interactive Protein Networks in Lower and Higher Species. Int J Mol Sci 2022; 23:ijms232214429. [PMID: 36430905 PMCID: PMC9697241 DOI: 10.3390/ijms232214429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
The phosphorylation of proteins affects their functions in extensively documented circumstances. However, the role of phosphorylation in many interactive networks of proteins remains very elusive due to the experimental limits of exploring the transient interaction in a large complex of assembled proteins induced by stimulation. Previous studies have suggested that phosphorylation is a recent evolutionary process that differently regulates ortholog proteins in numerous lineages of living organisms to create new functions. Despite the fact that numerous phospho-proteins have been compared between species, little is known about the organization of the full phospho-proteome, the role of phosphorylation to orchestrate large interactive networks of proteins, and the intertwined phospho-landscape in these networks. In this report, we aimed to investigate the acquired role of phosphate addition in the phenomenon of protein networking in different orders of living organisms. Our data highlighted the acquired status of phosphorylation in organizing large, connected assemblages in Homo sapiens. The protein networking guided by phosphorylation turned out to be prominent in humans, chaotic in yeast, and weak in flies. Furthermore, the molecular functions of GO annotation enrichment regulated by phosphorylation were found to be drastically different between flies, yeast, and humans, suggesting an evolutionary drift specific to each species.
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Affiliation(s)
- Claude Pasquier
- I3S, Université Côte d’Azur, Campus SophiaTech, CNRS, 06903 Nice, France
- Correspondence:
| | - Alain Robichon
- INRAE, ISA, Université Côte d’Azur, Campus SophiaTech, CNRS, 06903 Nice, France
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3
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Weigle AT, Feng J, Shukla D. Thirty years of molecular dynamics simulations on posttranslational modifications of proteins. Phys Chem Chem Phys 2022; 24:26371-26397. [PMID: 36285789 PMCID: PMC9704509 DOI: 10.1039/d2cp02883b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Posttranslational modifications (PTMs) are an integral component to how cells respond to perturbation. While experimental advances have enabled improved PTM identification capabilities, the same throughput for characterizing how structural changes caused by PTMs equate to altered physiological function has not been maintained. In this Perspective, we cover the history of computational modeling and molecular dynamics simulations which have characterized the structural implications of PTMs. We distinguish results from different molecular dynamics studies based upon the timescales simulated and analysis approaches used for PTM characterization. Lastly, we offer insights into how opportunities for modern research efforts on in silico PTM characterization may proceed given current state-of-the-art computing capabilities and methodological advancements.
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Affiliation(s)
- Austin T Weigle
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jiangyan Feng
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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4
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James Sanford E, Bustamante Smolka M. A field guide to the proteomics of post-translational modifications in DNA repair. Proteomics 2022; 22:e2200064. [PMID: 35695711 PMCID: PMC9950963 DOI: 10.1002/pmic.202200064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 05/19/2022] [Accepted: 05/30/2022] [Indexed: 12/15/2022]
Abstract
All cells incur DNA damage from exogenous and endogenous sources and possess pathways to detect and repair DNA damage. Post-translational modifications (PTMs), in the past 20 years, have risen to ineluctable importance in the study of the regulation of DNA repair mechanisms. For example, DNA damage response kinases are critical in both the initial sensing of DNA damage as well as in orchestrating downstream activities of DNA repair factors. Mass spectrometry-based proteomics revolutionized the study of the role of PTMs in the DNA damage response and has canonized PTMs as central modulators of nearly all aspects of DNA damage signaling and repair. This review provides a biologist-friendly guide for the mass spectrometry analysis of PTMs in the context of DNA repair and DNA damage responses. We reflect on the current state of proteomics for exploring new mechanisms of PTM-based regulation and outline a roadmap for designing PTM mapping experiments that focus on the DNA repair and DNA damage responses.
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Key Words
- LC-MS/MS, technology, bottom-up proteomics, technology, signal transduction, cell biology
- phosphoproteomics, technology, post-translational modification analysis, technology, post-translational modifications, cell biology, mass spectrometry
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Affiliation(s)
- Ethan James Sanford
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Marcus Bustamante Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853,Corresponding author:
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5
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Jonwal S, Verma N, Sinha AK. Regulation of photosynthetic light reaction proteins via reversible phosphorylation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 321:111312. [PMID: 35696912 DOI: 10.1016/j.plantsci.2022.111312] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/10/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
The regulation of photosynthesis occurs at different levels including the control of nuclear and plastid genes transcription, RNA processing and translation, protein translocation, assemblies and their post translational modifications. Out of all these, post translational modification enables rapid response of plants towards changing environmental conditions. Among all post-translational modifications, reversible phosphorylation is known to play a crucial role in the regulation of light reaction of photosynthesis. Although, phosphorylation of PS II subunits has been extensively studied but not much attention is given to other photosynthetic complexes such as PS I, Cytochrome b6f complex and ATP synthase. Phosphorylation reaction is known to protect photosynthetic apparatus in challenging environment conditions such as high light, elevated temperature, high salinity and drought. Recent studies have explored the role of photosynthetic protein phosphorylation in conferring plant immunity against the rice blast disease. The evolution of phosphorylation of different subunits of photosynthetic proteins occurred along with the evolution of plant lineage for their better adaptation to the changing environment conditions. In this review, we summarize the progress made in the research field of phosphorylation of photosynthetic proteins and highlights the missing links that need immediate attention.
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Affiliation(s)
- Sarvesh Jonwal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Neetu Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Alok Krishna Sinha
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
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6
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Zhuang X, Guo X, Gu T, Xu X, Qin L, Xu K, He Z, Zhang K. Phosphorylation of plant virus proteins: Analysis methods and biological functions. Front Microbiol 2022; 13:935735. [PMID: 35958157 PMCID: PMC9360750 DOI: 10.3389/fmicb.2022.935735] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Phosphorylation is one of the most extensively investigated post-translational modifications that orchestrate a variety of cellular signal transduction processes. The phosphorylation of virus-encoded proteins plays an important regulatory role in the infection cycle of such viruses in plants. In recent years, molecular mechanisms underlying the phosphorylation of plant viral proteins have been widely studied. Based on recent publications, our study summarizes the phosphorylation analyses of plant viral proteins and categorizes their effects on biological functions according to the viral life cycle. This review provides a theoretical basis for elucidating the molecular mechanisms of viral infection. Furthermore, it deepens our understanding of the biological functions of phosphorylation in the interactions between plants and viruses.
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Affiliation(s)
- Xinjian Zhuang
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Xiao Guo
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Tianxiao Gu
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Xiaowei Xu
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Lang Qin
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Kai Xu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhen He
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Kun Zhang
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China,Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China,*Correspondence: Kun Zhang, ;
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7
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Sowinski EE, Westman BM, Redmond CR, Kong Y, Olek AT, Olek J, McCann MC, Carpita NC. Lack of xyloglucan in the cell walls of the Arabidopsis xxt1/xxt2 mutant results in specific increases in homogalacturonan and glucomannan. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:212-227. [PMID: 35041247 DOI: 10.1111/tpj.15666] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/29/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Evan E Sowinski
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Bryce M Westman
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Celeste R Redmond
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Yingzhen Kong
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Anna T Olek
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Jan Olek
- Lyles School of Civil Engineering, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Maureen C McCann
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Nicholas C Carpita
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907, USA
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8
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Genies L, Martin L, Kanno S, Chiarenza S, Carasco L, Camilleri V, Vavasseur A, Henner P, Leonhardt N. Disruption of AtHAK/KT/KUP9 enhances plant cesium accumulation under low potassium supply. PHYSIOLOGIA PLANTARUM 2021; 173:1230-1243. [PMID: 34342899 DOI: 10.1111/ppl.13518] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Understanding the molecular mechanisms that underlie cesium (Cs+ ) transport in plants is important to limit the entry of its radioisotopes from contaminated areas into the food chain. The potentially toxic element Cs+ , which is not involved in any biological process, is chemically closed to the macronutrient potassium (K+ ). Among the multiple K+ carriers, the high-affinity K+ transporters family HAK/KT/KUP is thought to be relevant in mediating opportunistic Cs+ transport. Of the 13 KUP identified in A. thaliana, only HAK5, the major contributor to root K+ acquisition under low K+ supply, has been functionally demonstrated to be involved in Cs+ uptake in planta. In the present study, we showed that accumulation of Cs+ increased by up to 30% in two A. thaliana mutant lines lacking KUP9 and grown under low K+ supply. Since further experiments revealed that Cs+ release from contaminated plants to the external medium is proportionally lower in the two kup9 mutant alleles, we proposed that KUP9 disruption could impair Cs+ efflux. By contrast, K+ status in kup9 mutants is not affected, suggesting that KUP9 disruption does not alter substantially K+ transport in experimental conditions used. The putative primary role of KUP9 in plants is further discussed.
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Affiliation(s)
- Laure Genies
- Aix Marseille University, French Alternative Energies and Atomic Energy Commission (CEA), National Center for Scientific Research (CNRS), Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Laboratory of Signaling for the Adaptation to their Environment (SAVE), Saint-Paul-lez-Durance, France
- Laboratory of Research on Radionuclides Transfer Within Terrestrial Ecosystems (LR2T), Institute for Radiological Protection and Nuclear Safety (IRSN), Cadarache, France
| | - Ludovic Martin
- Aix Marseille University, French Alternative Energies and Atomic Energy Commission (CEA), National Center for Scientific Research (CNRS), Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Laboratory of Signaling for the Adaptation to their Environment (SAVE), Saint-Paul-lez-Durance, France
| | - Satomi Kanno
- Aix Marseille University, French Alternative Energies and Atomic Energy Commission (CEA), National Center for Scientific Research (CNRS), Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Laboratory of Signaling for the Adaptation to their Environment (SAVE), Saint-Paul-lez-Durance, France
| | - Serge Chiarenza
- Aix Marseille University, French Alternative Energies and Atomic Energy Commission (CEA), National Center for Scientific Research (CNRS), Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Laboratory of Signaling for the Adaptation to their Environment (SAVE), Saint-Paul-lez-Durance, France
| | - Loïc Carasco
- Laboratory of Research on Radionuclides Transfer Within Terrestrial Ecosystems (LR2T), Institute for Radiological Protection and Nuclear Safety (IRSN), Cadarache, France
| | - Virginie Camilleri
- Laboratory for Radionuclide Ecotoxicology (LECO), Institute for Radiological Protection and Nuclear Safety (IRSN), Cadarache, France
| | - Alain Vavasseur
- Aix Marseille University, French Alternative Energies and Atomic Energy Commission (CEA), National Center for Scientific Research (CNRS), Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Laboratory of Signaling for the Adaptation to their Environment (SAVE), Saint-Paul-lez-Durance, France
| | - Pascale Henner
- Laboratory of Research on Radionuclides Transfer Within Terrestrial Ecosystems (LR2T), Institute for Radiological Protection and Nuclear Safety (IRSN), Cadarache, France
| | - Nathalie Leonhardt
- Aix Marseille University, French Alternative Energies and Atomic Energy Commission (CEA), National Center for Scientific Research (CNRS), Bioscience and Biotechnology Institute of Aix-Marseille (BIAM), Laboratory of Signaling for the Adaptation to their Environment (SAVE), Saint-Paul-lez-Durance, France
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9
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Xue H, Zhang Q, Wang P, Cao B, Jia C, Cheng B, Shi Y, Guo WF, Wang Z, Liu ZX, Cheng H. qPTMplants: an integrative database of quantitative post-translational modifications in plants. Nucleic Acids Res 2021; 50:D1491-D1499. [PMID: 34718741 PMCID: PMC8728288 DOI: 10.1093/nar/gkab945] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/28/2021] [Accepted: 10/06/2021] [Indexed: 12/13/2022] Open
Abstract
As a crucial molecular mechanism, post-translational modifications (PTMs) play critical roles in a wide range of biological processes in plants. Recent advances in mass spectrometry-based proteomic technologies have greatly accelerated the profiling and quantification of plant PTM events. Although several databases have been constructed to store plant PTM data, a resource including more plant species and more PTM types with quantitative dynamics still remains to be developed. In this paper, we present an integrative database of quantitative PTMs in plants named qPTMplants (http://qptmplants.omicsbio.info), which hosts 1 242 365 experimentally identified PTM events for 429 821 nonredundant sites on 123 551 proteins under 583 conditions for 23 PTM types in 43 plant species from 293 published studies, with 620 509 quantification events for 136 700 PTM sites on 55 361 proteins under 354 conditions. Moreover, the experimental details, such as conditions, samples, instruments and methods, were manually curated, while a variety of annotations, including the sequence and structural characteristics, were integrated into qPTMplants. Then, various search and browse functions were implemented to access the qPTMplants data in a user-friendly manner. Overall, we anticipate that the qPTMplants database will be a valuable resource for further research on PTMs in plants.
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Affiliation(s)
- Han Xue
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Qingfeng Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Panqin Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Bijin Cao
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Chongchong Jia
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ben Cheng
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yuhua Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Wei-Feng Guo
- School of Electrical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Zhenlong Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ze-Xian Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Han Cheng
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
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10
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Computational Phosphorylation Network Reconstruction: An Update on Methods and Resources. Methods Mol Biol 2021. [PMID: 34270057 DOI: 10.1007/978-1-0716-1625-3_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: 11/19/2023]
Abstract
Most proteins undergo some form of modification after translation, and phosphorylation is one of the most relevant and ubiquitous post-translational modifications. The succession of protein phosphorylation and dephosphorylation catalyzed by protein kinase and phosphatase, respectively, constitutes a key mechanism of molecular information flow in cellular systems. The protein interactions of kinases, phosphatases, and their regulatory subunits and substrates are the main part of phosphorylation networks. To elucidate the landscape of phosphorylation events has been a central goal pursued by both experimental and computational approaches. Substrate specificity (e.g., sequence, structure) or the phosphoproteome has been utilized in an array of different statistical learning methods to infer phosphorylation networks. In this chapter, different computational phosphorylation network inference-related methods and resources are summarized and discussed.
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11
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Gupta C, Ramegowda V, Basu S, Pereira A. Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought Resistance. Front Genet 2021; 12:652189. [PMID: 34249082 PMCID: PMC8264776 DOI: 10.3389/fgene.2021.652189] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/13/2021] [Indexed: 12/13/2022] Open
Abstract
Gene regulatory networks underpin stress response pathways in plants. However, parsing these networks to prioritize key genes underlying a particular trait is challenging. Here, we have built the Gene Regulation and Association Network (GRAiN) of rice (Oryza sativa). GRAiN is an interactive query-based web-platform that allows users to study functional relationships between transcription factors (TFs) and genetic modules underlying abiotic-stress responses. We built GRAiN by applying a combination of different network inference algorithms to publicly available gene expression data. We propose a supervised machine learning framework that complements GRAiN in prioritizing genes that regulate stress signal transduction and modulate gene expression under drought conditions. Our framework converts intricate network connectivity patterns of 2160 TFs into a single drought score. We observed that TFs with the highest drought scores define the functional, structural, and evolutionary characteristics of drought resistance in rice. Our approach accurately predicted the function of OsbHLH148 TF, which we validated using in vitro protein-DNA binding assays and mRNA sequencing loss-of-function mutants grown under control and drought stress conditions. Our network and the complementary machine learning strategy lends itself to predicting key regulatory genes underlying other agricultural traits and will assist in the genetic engineering of desirable rice varieties.
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Affiliation(s)
- Chirag Gupta
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Venkategowda Ramegowda
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Supratim Basu
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Andy Pereira
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
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12
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Juarez-Escobar J, Elizalde-Contreras JM, Loyola-Vargas VM, Ruiz-May E. A Phosphoproteomic Analysis Pipeline for Peels of Tropical Fruits. Methods Mol Biol 2021; 2139:179-196. [PMID: 32462587 DOI: 10.1007/978-1-0716-0528-8_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Phosphorylation is a posttranslational reversible modification related to signaling and regulatory mechanisms. Protein phosphorylation is linked to structural changes that modulate protein activity, interaction, or localization and therefore the cell signaling pathways. The use of techniques for phosphoprotein enrichment along with mass spectrometry has become a powerful tool for the characterization of signal transduction in model organisms. However, limited efforts have focused on the establishment of protocols for the analysis of the phosphoproteome in nonmodel organisms such as tropical fruits. This chapter describes a potential pipeline for sample preparation and enrichment of phosphorylated proteins/peptides before MS analysis of peels of some species of tropical fruits.
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Affiliation(s)
- Janet Juarez-Escobar
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Veracruz, Mexico
| | - José M Elizalde-Contreras
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Veracruz, Mexico
| | - Víctor M Loyola-Vargas
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán (CICY), Mérida, Yucatán, Mexico
| | - Eliel Ruiz-May
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Veracruz, Mexico.
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13
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Xi L, Zhang Z, Herold S, Kassem S, Wu XN, Schulze WX. Phosphorylation Site Motifs in Plant Protein Kinases and Their Substrates. Methods Mol Biol 2021; 2358:1-16. [PMID: 34270043 DOI: 10.1007/978-1-0716-1625-3_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Protein phosphorylation is an important cellular regulatory mechanism affecting the activity, localization, conformation, and interaction of proteins. Protein phosphorylation is catalyzed by kinases, and thus kinases are the enzymes regulating cellular signaling cascades. In the model plant Arabidopsis, 940 genes encode for kinases. The substrate proteins of kinases are phosphorylated at defined sites, which consist of common patterns around the phosphorylation site, known as phosphorylation motifs. The discovery of kinase specificity with a preference of phosphorylation of certain motifs and application of such motifs in deducing signaling cascades helped to reveal underlying regulation mechanisms, and facilitated the prediction of kinase-target pairs. In this mini-review, we took advantage of retrieved data as examples to present the functions of kinase families along with their commonly found phosphorylation motifs from their substrates.
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Affiliation(s)
- Lin Xi
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany.
| | - Zhaoxia Zhang
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Sandra Herold
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Sarah Kassem
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Xu Na Wu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
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Gupta C, Ramegowda V, Basu S, Pereira A. Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought Resistance. Front Genet 2021. [PMID: 34249082 DOI: 10.1101/2020.04.29.068379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
Gene regulatory networks underpin stress response pathways in plants. However, parsing these networks to prioritize key genes underlying a particular trait is challenging. Here, we have built the Gene Regulation and Association Network (GRAiN) of rice (Oryza sativa). GRAiN is an interactive query-based web-platform that allows users to study functional relationships between transcription factors (TFs) and genetic modules underlying abiotic-stress responses. We built GRAiN by applying a combination of different network inference algorithms to publicly available gene expression data. We propose a supervised machine learning framework that complements GRAiN in prioritizing genes that regulate stress signal transduction and modulate gene expression under drought conditions. Our framework converts intricate network connectivity patterns of 2160 TFs into a single drought score. We observed that TFs with the highest drought scores define the functional, structural, and evolutionary characteristics of drought resistance in rice. Our approach accurately predicted the function of OsbHLH148 TF, which we validated using in vitro protein-DNA binding assays and mRNA sequencing loss-of-function mutants grown under control and drought stress conditions. Our network and the complementary machine learning strategy lends itself to predicting key regulatory genes underlying other agricultural traits and will assist in the genetic engineering of desirable rice varieties.
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Affiliation(s)
- Chirag Gupta
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Venkategowda Ramegowda
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Supratim Basu
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Andy Pereira
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
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15
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PhosPhAt 4.0: An Updated Arabidopsis Database for Searching Phosphorylation Sites and Kinase-Target Interactions. Methods Mol Biol 2021; 2358:189-202. [PMID: 34270056 DOI: 10.1007/978-1-0716-1625-3_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The PhosPhAt 4.0 database contains information on Arabidopsis phosphorylation sites identified by mass spectrometry in large-scale experiments from different research groups. So far PhosPhAt 4.0 has been one of the most significant large-scale data resources for plant phosphorylation studies. Functionalities of the web application, besides display of phosphorylation sites, include phosphorylation site prediction and kinase-target relationships retrieval. Here, we present an overview and user instructions for the PhosPhAt 4.0 database, with strong emphasis on recent renewals regarding protein annotation by SUBA4.0 and Mapman4, and additional phosphorylation site information imported from other databases, such as UniProt. Here, we provide a user guide for the retrieval of phosphorylation motifs from the kinase-target database and how to visualize these results. The improvements incorporated into the PhosPhAt 4.0 database have produced much more functionality and user flexibility for phosphoproteomic analysis.
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Abstract
Plants are an important part of nature because as photoautotrophs, they provide a nutrient source for many other living organisms. Due to their sessile nature, to overcome both biotic and abiotic stresses, plants have developed intricate mechanisms for perception of and reaction to these stresses, both on an external level (perception) and on an internal level (reaction). Specific proteins found within cells play crucial roles in stress mitigation by enhancing cellular processes that facilitate the plants survival during the unfavorable conditions. Well before plants are able to synthesize nascent proteins in response to stress, proteins which already exist in the cell can be subjected to an array of posttranslation modifications (PTMs) that permit a rapid response. These activated proteins can, in turn, aid in further stress responses. Different PTMs have different functions in growth and development of plants. Protein phosphorylation, a reversible form of modification has been well elucidated, and its role in signaling cascades is well documented. In this mini-review, we discuss the integration of protein phosphorylation with other components of abiotic stress-responsive pathways including phytohormones and ion homeostasis. Overall, this review demonstrates the high interconnectivity of the stress response system in plants and how readily plants are able to toggle between various signaling pathways in order to survive harsh conditions. Most notably, fluctuations of the cytosolic calcium levels seem to be a linking component of the various signaling pathways.
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Affiliation(s)
- Rebecca Njeri Damaris
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Science, Hubei University, Wuhan, China
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Science, Hubei University, Wuhan, China.
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17
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Comparative phosphoproteomic analysis of BR-defective mutant reveals a key role of GhSK13 in regulating cotton fiber development. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1905-1917. [PMID: 32632733 DOI: 10.1007/s11427-020-1728-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/12/2020] [Indexed: 02/07/2023]
Abstract
Brassinosteroid (BR), a steroid phytohormone, whose signaling transduction pathways include a series of phosphorylation and dephosphorylation events, and GSK3s are the main negative regulator kinases. BRs have been shown to play vital roles in cotton fiber elongation. However, the underlying mechanism is still elusive. In this study, fibers of a BR-defective mutant Pagoda 1 (pag1), and its corresponding wild-type (ZM24) were selected for a comparative global phosphoproteome analysis at critical developmental time points: fast-growing stage (10 days after pollination (DPA)) and secondary cell wall synthesis stage (20 DPA). Based on the substrate characteristics of GSK3, 900 potential substrates were identified. Their GO and KEGG annotation results suggest that BR functions in fiber development by regulating GhSKs (GSK3s of Gossypium hirsutum L.) involved microtubule cytoskeleton organization, and pathways of glucose, sucrose and lipid metabolism. Further experimental results revealed that among the GhSK members identified, GhSK13 not only plays a role in BR signaling pathway, but also functions in developing fiber by respectively interacting with an AP2-like ethylene-responsive factor GhAP2L, a nuclear transcription factor Gh_DNF_YB19, and a homeodomain zipper member GhHDZ5. Overall, our phosphoproteomic research advances the understanding of fiber development controlled by BR signal pathways especially through GhSKs, and also offers numbers of target proteins for improving cotton fiber quality.
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18
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Shi Y, Zhang Y, Lin S, Wang C, Zhou J, Peng D, Xue Y. dbPSP 2.0, an updated database of protein phosphorylation sites in prokaryotes. Sci Data 2020; 7:164. [PMID: 32472030 PMCID: PMC7260176 DOI: 10.1038/s41597-020-0506-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 04/30/2020] [Indexed: 12/20/2022] Open
Abstract
In prokaryotes, protein phosphorylation plays a critical role in regulating a broad spectrum of biological processes and occurs mainly on various amino acids, including serine (S), threonine (T), tyrosine (Y), arginine (R), aspartic acid (D), histidine (H) and cysteine (C) residues of protein substrates. Through literature curation and public database integration, here we reported an updated database of phosphorylation sites (p-sites) in prokaryotes (dbPSP 2.0) that contains 19,296 experimentally identified p-sites in 8,586 proteins from 200 prokaryotic organisms, which belong to 12 phyla of two kingdoms, bacteria and archaea. To carefully annotate these phosphoproteins and p-sites, we integrated the knowledge from 88 publicly available resources that covers 9 aspects, namely, taxonomy annotation, genome annotation, function annotation, transcriptional regulation, sequence and structure information, family and domain annotation, interaction, orthologous information and biological pathway. In contrast to version 1.0 (~30 MB), dbPSP 2.0 contains ~9 GB of data, with a 300-fold increased volume. We anticipate that dbPSP 2.0 can serve as a useful data resource for further investigating phosphorylation events in prokaryotes. dbPSP 2.0 is free for all users to access at: http://dbpsp.biocuckoo.cn.
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Affiliation(s)
- Ying Shi
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Ying Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Shaofeng Lin
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Chenwei Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Jiaqi Zhou
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Di Peng
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
| | - Yu Xue
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
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Facciuolo A, Denomy C, Lipsit S, Kusalik A, Napper S. From Beef to Bees: High-Throughput Kinome Analysis to Understand Host Responses of Livestock Species to Infectious Diseases and Industry-Associated Stress. Front Immunol 2020; 11:765. [PMID: 32499776 PMCID: PMC7243914 DOI: 10.3389/fimmu.2020.00765] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/06/2020] [Indexed: 11/13/2022] Open
Abstract
Within human health research, the remarkable utility of kinase inhibitors as therapeutics has motivated efforts to understand biology at the level of global cellular kinase activity (the kinome). In contrast, the diminished potential for using kinase inhibitors in food animals has dampened efforts to translate this research approach to livestock species. This, in our opinion, was a lost opportunity for livestock researchers given the unique potential of kinome analysis to offer insight into complex biology. To remedy this situation, our lab developed user-friendly, cost-effective approaches for kinome analysis that can be readily incorporated into most research programs but with a specific priority to enable the technology to livestock researchers. These contributions include the development of custom software programs for the creation of species-specific kinome arrays as well as comprehensive deconvolution and analysis of kinome array data. Presented in this review are examples of the application of kinome analysis to highlight the utility of the technology to further our understanding of two key complex biological events of priority to the livestock industry: host immune responses to infectious diseases and animal stress responses. These advances and examples of application aim to provide both mechanisms and motivation for researchers, particularly livestock researchers, to incorporate kinome analysis into their research programs.
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Affiliation(s)
- Antonio Facciuolo
- Vaccine and Infectious Disease Organization - International Vaccine Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Connor Denomy
- Vaccine and Infectious Disease Organization - International Vaccine Centre, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Sean Lipsit
- Vaccine and Infectious Disease Organization - International Vaccine Centre, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Anthony Kusalik
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Scott Napper
- Vaccine and Infectious Disease Organization - International Vaccine Centre, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
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20
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Lin S, Wang C, Zhou J, Shi Y, Ruan C, Tu Y, Yao L, Peng D, Xue Y. EPSD: a well-annotated data resource of protein phosphorylation sites in eukaryotes. Brief Bioinform 2020; 22:298-307. [PMID: 32008039 DOI: 10.1093/bib/bbz169] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/25/2019] [Accepted: 12/10/2019] [Indexed: 12/16/2022] Open
Abstract
As an important post-translational modification (PTM), protein phosphorylation is involved in the regulation of almost all of biological processes in eukaryotes. Due to the rapid progress in mass spectrometry-based phosphoproteomics, a large number of phosphorylation sites (p-sites) have been characterized but remain to be curated. Here, we briefly summarized the current progresses in the development of data resources for the collection, curation, integration and annotation of p-sites in eukaryotic proteins. Also, we designed the eukaryotic phosphorylation site database (EPSD), which contained 1 616 804 experimentally identified p-sites in 209 326 phosphoproteins from 68 eukaryotic species. In EPSD, we not only collected 1 451 629 newly identified p-sites from high-throughput (HTP) phosphoproteomic studies, but also integrated known p-sites from 13 additional databases. Moreover, we carefully annotated the phosphoproteins and p-sites of eight model organisms by integrating the knowledge from 100 additional resources that covered 15 aspects, including phosphorylation regulator, genetic variation and mutation, functional annotation, structural annotation, physicochemical property, functional domain, disease-associated information, protein-protein interaction, drug-target relation, orthologous information, biological pathway, transcriptional regulator, mRNA expression, protein expression/proteomics and subcellular localization. We anticipate that the EPSD can serve as a useful resource for further analysis of eukaryotic phosphorylation. With a data volume of 14.1 GB, EPSD is free for all users at http://epsd.biocuckoo.cn/.
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Affiliation(s)
| | | | - Jiaqi Zhou
- Huazhong University of Science and Technology
| | - Ying Shi
- Huazhong University of Science and Technology
| | - Chen Ruan
- Huazhong University of Science and Technology
| | - Yiran Tu
- Huazhong University of Science and Technology
| | - Lan Yao
- Huazhong University of Science and Technology
| | - Di Peng
- Huazhong University of Science and Technology
| | - Yu Xue
- Huazhong University of Science and Technology
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21
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Calvo P, Gagliano M, Souza GM, Trewavas A. Plants are intelligent, here's how. ANNALS OF BOTANY 2020; 125:11-28. [PMID: 31563953 PMCID: PMC6948212 DOI: 10.1093/aob/mcz155] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 07/01/2019] [Accepted: 09/26/2019] [Indexed: 05/07/2023]
Abstract
HYPOTHESES The drive to survive is a biological universal. Intelligent behaviour is usually recognized when individual organisms including plants, in the face of fiercely competitive or adverse, real-world circumstances, change their behaviour to improve their probability of survival. SCOPE This article explains the potential relationship of intelligence to adaptability and emphasizes the need to recognize individual variation in intelligence showing it to be goal directed and thus being purposeful. Intelligent behaviour in single cells and microbes is frequently reported. Individual variation might be underpinned by a novel learning mechanism, described here in detail. The requirements for real-world circumstances are outlined, and the relationship to organic selection is indicated together with niche construction as a good example of intentional behaviour that should improve survival. Adaptability is important in crop development but the term may be complex incorporating numerous behavioural traits some of which are indicated. CONCLUSION There is real biological benefit to regarding plants as intelligent both from the fundamental issue of understanding plant life but also from providing a direction for fundamental future research and in crop breeding.
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Affiliation(s)
- Paco Calvo
- Minimal Intelligence Laboratory, Universidad de Murcia, Murcia, Spain
| | - Monica Gagliano
- Biological Intelligence Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Gustavo M Souza
- Laboratory of Plant Cognition and Electrophysiology, Federal University of Pelotas, Pelotas - RS, Brazil
| | - Anthony Trewavas
- Institute of Molecular Plant Science, Kings Buildings, University of Edinburgh, Edinburgh, UK
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22
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Zhang B, Chen J, Zong J, Yan X, Liu J. Unbiased phosphoproteome profiling uncovers novel phosphoproteins and phosphorylation motifs in bermudagrass stolons. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 144:92-99. [PMID: 31561202 DOI: 10.1016/j.plaphy.2019.09.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/06/2019] [Accepted: 09/21/2019] [Indexed: 05/20/2023]
Abstract
As a widely used turfgrass species, bermudagrass (Cynodon dactylon L.) can be easily propagated through colonial growth of stolons. Previous studies collectively revealed that exotic environmental factors and intrinsic hormones and genes are all involved in the differentiation, development, and diageotropical growth of stolons. However, the detailed molecular mechanism how environmental and hormone signals regulate the gene expression and biochemical activities in bermudagrass stolons remains unclear. In this study, we observed that reversible phosphorylation modification plays important roles in normal growth and physiological functions of bermudagrass stolons. LC-MS/MS analyses of the total protein extracts of bermudagrass stolons without preliminary phosphopeptide-enrichment successfully identified 646 nonredundant phosphorylation sites and 485 phosphoproteins. The phosphoproteins were significantly enriched in protein phosphorylation regulation and starch metabolism processes. Motif-X analyses further revealed that phosphoproteins containing novel phosphorylation motifs might be involved in transcription regulation of bermudagrass stolons. These results greatly expanded our understanding of the growth and development of bermudagrass stolons at the post-translational level.
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Affiliation(s)
- Bing Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
| | - Jingbo Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Junqin Zong
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Xuebing Yan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Jianxiu Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
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23
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Hu B, Wang N, Bi X, Karaaslan ES, Weber AL, Zhu W, Berendzen KW, Liu C. Plant lamin-like proteins mediate chromatin tethering at the nuclear periphery. Genome Biol 2019; 20:87. [PMID: 31039799 PMCID: PMC6492433 DOI: 10.1186/s13059-019-1694-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 04/16/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The nuclear envelope not only serves as a physical barrier separating nuclear content from the cytoplasm but also plays critical roles in modulating the three-dimensional organization of genomic DNA. For both plants and animals, the nuclear periphery is a functional compartment enriched with heterochromatin. To date, how plants manage to selectively tether chromatin at the nuclear periphery is unclear. RESULTS By conducting dual-color fluorescence in situ hybridization experiments on 2C nuclei, we show that in Arabidopsis thaliana, specific chromatin positioning at the nuclear periphery requires plant lamin-like proteins CROWDED NUCLEI 1 (CRWN1), CRWN4, and DNA methylation in CHG and CHH contexts. With chromosome painting and Hi-C analyses, we show global attenuation of spatial chromatin compartmentalization and chromatin positioning patterns at the nuclear periphery in both the crwn1 and crwn4 mutants. Furthermore, ChIP-seq analysis indicates that CRWN1 directly interacts with chromatin domains localized at the nuclear periphery, which mainly contains non-accessible chromatin. CONCLUSIONS In summary, we conclude that CRWN1 is a key component of the lamina-chromatin network in plants. It is functionally equivalent to animal lamins, playing critical roles in modulating patterns of chromatin positioning at the nuclear periphery.
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Affiliation(s)
- Bo Hu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Nan Wang
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Xiuli Bi
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Ezgi Süheyla Karaaslan
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Anna-Lena Weber
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Wangsheng Zhu
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Kenneth Wayne Berendzen
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany.
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24
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Subba P, Narayana Kotimoole C, Prasad TSK. Plant Proteome Databases and Bioinformatic Tools: An Expert Review and Comparative Insights. ACTA ACUST UNITED AC 2019; 23:190-206. [DOI: 10.1089/omi.2019.0024] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Pratigya Subba
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Chinmaya Narayana Kotimoole
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Thottethodi Subrahmanya Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
- Institute of Bioinformatics, International Technology Park, Bangalore, India
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25
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Deng W, Ma L, Zhang Y, Zhou J, Wang Y, Liu Z, Xue Y. THANATOS: an integrative data resource of proteins and post-translational modifications in the regulation of autophagy. Autophagy 2019; 14:296-310. [PMID: 29157087 DOI: 10.1080/15548627.2017.1402990] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Macroautophagy/autophagy is a highly conserved process for degrading cytoplasmic contents, determines cell survival or death, and regulates the cellular homeostasis. Besides ATG proteins, numerous regulators together with various post-translational modifications (PTMs) are also involved in autophagy. In this work, we collected 4,237 experimentally identified proteins regulated in autophagy and cell death pathways from the literature. Then we computationally identified potential orthologs of known proteins, and developed a comprehensive database of The Autophagy, Necrosis, ApopTosis OrchestratorS (THANATOS, http://thanatos.biocuckoo.org ), containing 191,543 proteins potentially associated with autophagy and cell death pathways in 164 eukaryotes. We performed an evolutionary analysis of ATG genes, and observed that ATGs required for the autophagosome formation are highly conserved across eukaryotes. Further analyses revealed that known cancer genes and drug targets were overrepresented in human autophagy proteins, which were significantly associated in a number of signaling pathways and human diseases. By reconstructing a human kinase-substrate phosphorylation network for ATG proteins, our results confirmed that phosphorylation play a critical role in regulating autophagy. In total, we mapped 65,015 known sites of 11 types of PTMs to collected proteins, and revealed that all types of PTM substrates were enriched in human autophagy. In addition, we observed multiple types of PTM regulators such as protein kinases and ubiquitin E3 ligases or adaptors were significantly associated with human autophagy, and again the results emphasized the importance of PTM regulations in autophagy. We anticipated THANATOS can be a useful resource for further studies.
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Affiliation(s)
- Wankun Deng
- a Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
| | - Lili Ma
- a Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
| | - Ying Zhang
- a Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
| | - Jiaqi Zhou
- a Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
| | - Yongbo Wang
- a Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
| | - Zexian Liu
- a Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China.,b State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine , Sun Yat-sen University Cancer Center , 651 Dongfeng Road East, 510060 , Guangzhou , Guangdong , P. R. China
| | - Yu Xue
- a Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
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26
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Zwiewka M, Bilanovičová V, Seifu YW, Nodzyński T. The Nuts and Bolts of PIN Auxin Efflux Carriers. FRONTIERS IN PLANT SCIENCE 2019; 10:985. [PMID: 31417597 PMCID: PMC6685051 DOI: 10.3389/fpls.2019.00985] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/12/2019] [Indexed: 05/20/2023]
Abstract
The plant-specific proteins named PIN-FORMED (PIN) efflux carriers facilitate the direction of auxin flow and thus play a vital role in the establishment of local auxin maxima within plant tissues that subsequently guide plant ontogenesis. They are membrane integral proteins with two hydrophobic regions consisting of alpha-helices linked with a hydrophilic loop, which is usually longer for the plasma membrane-localized PINs. The hydrophilic loop harbors molecular cues important for the subcellular localization and thus auxin efflux function of those transporters. The three-dimensional structure of PIN has not been solved yet. However, there are scattered but substantial data concerning the functional characterization of amino acid strings that constitute these carriers. These sequences include motifs vital for vesicular trafficking, residues regulating membrane diffusion, cellular polar localization, and activity of PINs. Here, we summarize those bits of information striving to provide a reference to structural motifs that have been investigated experimentally hoping to stimulate the efforts toward unraveling of PIN structure-function connections.
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27
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Arsova B, Watt M, Usadel B. Monitoring of Plant Protein Post-translational Modifications Using Targeted Proteomics. FRONTIERS IN PLANT SCIENCE 2018; 9:1168. [PMID: 30174677 PMCID: PMC6107839 DOI: 10.3389/fpls.2018.01168] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/23/2018] [Indexed: 05/19/2023]
Abstract
Protein post-translational modifications (PTMs) are among the fastest and earliest of plant responses to changes in the environment, making the mechanisms and dynamics of PTMs an important area of plant science. One of the most studied PTMs is protein phosphorylation. This review summarizes the use of targeted proteomics for the elucidation of the biological functioning of plant PTMs, and focuses primarily on phosphorylation. Since phosphorylated peptides have a low abundance, usually complex enrichment protocols are required for their research. Initial identification is usually performed with discovery phosphoproteomics, using high sensitivity mass spectrometers, where as many phosphopeptides are measured as possible. Once a PTM site is identified, biological characterization can be addressed with targeted proteomics. In targeted proteomics, Selected/Multiple Reaction Monitoring (S/MRM) is traditionally coupled to simple, standard protein digestion protocols, often omitting the enrichment step, and relying on triple-quadruple mass spectrometer. The use of synthetic peptides as internal standards allows accurate identification, avoiding cross-reactivity typical for some antibody based approaches. Importantly, internal standards allow absolute peptide quantitation, reported down to 0.1 femtomoles, also useful for determination of phospho-site occupancy. S/MRM is advantageous in situations where monitoring and diagnostics of peptide PTM status is needed for many samples, as it has faster sample processing times, higher throughput than other approaches, and excellent quantitation and reproducibility. Furthermore, the number of publicly available data-bases with plant PTM discovery data is growing, facilitating selection of modified peptides and design of targeted proteomics workflows. Recent instrument developments result in faster scanning times, inclusion of ion-trap instruments leading to parallel reaction monitoring- which further facilitates S/MRM experimental design. Finally, recent combination of data independent and data dependent spectra acquisition means that in addition to anticipated targeted data, spectra can now be queried for unanticipated information. The potential for future applications in plant biology is outlined.
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Affiliation(s)
- Borjana Arsova
- Institut für Bio- und Geowissenschaften, IBG-2–Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
| | - Michelle Watt
- Institut für Bio- und Geowissenschaften, IBG-2–Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
| | - Björn Usadel
- Institut für Bio- und Geowissenschaften, IBG-2–Plant Sciences, Forschungszentrum Jülich, Jülich, Germany
- IBMG: Institute for Biology I, RWTH Aachen University, Aachen, Germany
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Abstract
Advancements in MS-based phospho-proteomics techniques have helped uncover hundred thousands of protein phosphorylation sites in human and various model organisms. The majority of these sites are uncharacterized. The sheer number of uncharacterized sites necessitates systematic approaches to prioritize sites for more in-depth annotation. Analyzing the phosphorylation and sequence conservation of uncharacterized sites across species can help reveal a subset of the functionally important phosphorylation events. Here, we outline the workflow and provide an overview of publicly available computational resources for conservation analysis of novel phosphorylation sites.
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Bai Y, Chen B, Li M, Zhou Y, Ren S, Xu Q, Chen M, Wang S. FPD: A comprehensive phosphorylation database in fungi. Fungal Biol 2017; 121:869-875. [DOI: 10.1016/j.funbio.2017.06.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 06/09/2017] [Accepted: 06/18/2017] [Indexed: 12/26/2022]
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Almadanim MC, Alexandre BM, Rosa MTG, Sapeta H, Leitão AE, Ramalho JC, Lam TT, Negrão S, Abreu IA, Oliveira MM. Rice calcium-dependent protein kinase OsCPK17 targets plasma membrane intrinsic protein and sucrose-phosphate synthase and is required for a proper cold stress response. PLANT, CELL & ENVIRONMENT 2017; 40:1197-1213. [PMID: 28102545 DOI: 10.1111/pce.12916] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/10/2017] [Accepted: 01/15/2017] [Indexed: 05/20/2023]
Abstract
Calcium-dependent protein kinases (CDPKs) are involved in plant tolerance mechanisms to abiotic stresses. Although CDPKs are recognized as key messengers in signal transduction, the specific role of most members of this family remains unknown. Here, we test the hypothesis that OsCPK17 plays a role in rice cold stress response by analysing OsCPK17 knockout, silencing and overexpressing rice lines under low temperature. Altered OsCPK17 gene expression compromises cold tolerance performance, without affecting the expression of key cold stress-inducible genes. A comparative phosphoproteomic approach led to the identification of six potential in vivo OsCPK17 targets, which are associated with sugar and nitrogen metabolism, and with osmotic regulation. To test direct interaction, in vitro kinase assays were performed, showing that the sucrose-phosphate synthase OsSPS4 and the aquaporin OsPIP2;1/OsPIP2;6 are phosphorylated by OsCPK17 in a calcium-dependent manner. Altogether, our data indicates that OsCPK17 is required for a proper cold stress response in rice, likely affecting the activity of membrane channels and sugar metabolism.
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Affiliation(s)
- M Cecília Almadanim
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - Bruno M Alexandre
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
| | - Margarida T G Rosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - Helena Sapeta
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - António E Leitão
- Plant Stress and Biodiversity, Linking Landscape, Environment, Agriculture and Food (LEAF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia, Universidade de Lisboa, 2784-505, Oeiras, Portugal
| | - José C Ramalho
- Plant Stress and Biodiversity, Linking Landscape, Environment, Agriculture and Food (LEAF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia, Universidade de Lisboa, 2784-505, Oeiras, Portugal
| | - TuKiet T Lam
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520-8024, USA
- MS and Proteomics Resource, WM Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, CT, 06520-8024, USA
| | - Sónia Negrão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Isabel A Abreu
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
| | - M Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, 2780-157, Oeiras, Portugal
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Roy BC, Mukherjee A. Computational analysis of the glutamate receptor gene family of Arabidopsis thaliana. J Biomol Struct Dyn 2016; 35:2454-2474. [PMID: 27632363 DOI: 10.1080/07391102.2016.1222968] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Bidhan Chandra Roy
- Department of Botany, Dinabandhu Mahavidyalaya, North 24 Parganas, Bongaon, West Bengal 743235, India
| | - Ashutosh Mukherjee
- Department of Botany, Vivekananda College, 269, Diamond Harbour Road, Thakurpukur, Kolkata, West Bengal 700063, India
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Grieco M, Jain A, Ebersberger I, Teige M. An evolutionary view on thylakoid protein phosphorylation uncovers novel phosphorylation hotspots with potential functional implications. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3883-96. [PMID: 27117338 DOI: 10.1093/jxb/erw164] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The regulation of photosynthetic light reactions by reversible protein phosphorylation is well established today, but functional studies have so far mostly been restricted to processes affecting light-harvesting complex II and the core proteins of photosystem II. Virtually no functional data are available on regulatory effects at the other photosynthetic complexes despite the identification of multiple phosphorylation sites. Therefore we summarize the available data from 50 published phospho-proteomics studies covering the main complexes involved in photosynthetic light reactions in the 'green lineage' (i.e. green algae and land plants) as well as its cyanobacterial counterparts. In addition, we performed an extensive orthologue search for the major photosynthetic thylakoid proteins in 41 sequenced genomes and generated sequence alignments to survey the phylogenetic distribution of phosphorylation sites and their evolutionary conservation from green algae to higher plants. We observed a number of uncharacterized phosphorylation hotspots at photosystem I and the ATP synthase with potential functional relevance as well as an unexpected divergence of phosphosites. Although technical limitations might account for a number of those differences, we think that many of these phosphosites have important functions. This is particularly important for mono- and dicot plants, where these sites might be involved in regulatory processes such as stress acclimation.
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Affiliation(s)
- Michele Grieco
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstr. 14, A-1090 Vienna, Austria
| | - Arpit Jain
- Department for Applied Bioinformatics, Institute for Cell Biology and Neuroscience, Goethe University, Max-von-Laue Str. 13, D-60438 Frankfurt, Germany
| | - Ingo Ebersberger
- Department for Applied Bioinformatics, Institute for Cell Biology and Neuroscience, Goethe University, Max-von-Laue Str. 13, D-60438 Frankfurt, Germany Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Anlage 25, D-60325 Frankfurt, Germany
| | - Markus Teige
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstr. 14, A-1090 Vienna, Austria
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Ullah S, Lin S, Xu Y, Deng W, Ma L, Zhang Y, Liu Z, Xue Y. dbPAF: an integrative database of protein phosphorylation in animals and fungi. Sci Rep 2016; 6:23534. [PMID: 27010073 PMCID: PMC4806352 DOI: 10.1038/srep23534] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/08/2016] [Indexed: 12/26/2022] Open
Abstract
Protein phosphorylation is one of the most important post-translational modifications (PTMs) and regulates a broad spectrum of biological processes. Recent progresses in phosphoproteomic identifications have generated a flood of phosphorylation sites, while the integration of these sites is an urgent need. In this work, we developed a curated database of dbPAF, containing known phosphorylation sites in H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. pombe and S. cerevisiae. From the scientific literature and public databases, we totally collected and integrated 54,148 phosphoproteins with 483,001 phosphorylation sites. Multiple options were provided for accessing the data, while original references and other annotations were also present for each phosphoprotein. Based on the new data set, we computationally detected significantly over-represented sequence motifs around phosphorylation sites, predicted potential kinases that are responsible for the modification of collected phospho-sites, and evolutionarily analyzed phosphorylation conservation states across different species. Besides to be largely consistent with previous reports, our results also proposed new features of phospho-regulation. Taken together, our database can be useful for further analyses of protein phosphorylation in human and other model organisms. The dbPAF database was implemented in PHP + MySQL and freely available at http://dbpaf.biocuckoo.org.
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Affiliation(s)
- Shahid Ullah
- Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Shaofeng Lin
- Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yang Xu
- Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Wankun Deng
- Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Lili Ma
- Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Ying Zhang
- Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Zexian Liu
- Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yu Xue
- Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.,Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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Nguyen TN, Son S, Jordan MC, Levin DB, Ayele BT. Lignin biosynthesis in wheat (Triticum aestivum L.): its response to waterlogging and association with hormonal levels. BMC PLANT BIOLOGY 2016; 16:28. [PMID: 26811086 PMCID: PMC4727291 DOI: 10.1186/s12870-016-0717-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 01/18/2016] [Indexed: 05/07/2023]
Abstract
BACKGROUND Lignin is an important structural component of plant cell wall that confers mechanical strength and tolerance against biotic and abiotic stressors; however it affects the use of biomass such as wheat straw for some industrial applications such as biofuel production. Genetic alteration of lignin quantity and quality has been considered as a viable option to overcome this problem. However, the molecular mechanisms underlying lignin formation in wheat biomass has not been studied. Combining molecular and biochemical approaches, the present study investigated the transcriptional regulation of lignin biosynthesis in two wheat cultivars with varying lodging characteristics and also in response to waterlogging. It also examined the association of lignin level in tissues with that of plant hormones implicated in the control of lignin biosynthesis. RESULTS Analysis of lignin biosynthesis in the two wheat cultivars revealed a close association of lodging resistance with internode lignin content and expression of 4-coumarate:CoA ligase1 (4CL1), p-coumarate 3-hydroxylase1 (C3H1), cinnamoyl-CoA reductase2 (CCR2), ferulate 5-hydroxylase2 (F5H2) and caffeic acid O-methyltransferase2 (COMT2), which are among the genes highly expressed in wheat tissues, implying the importance of these genes in mediating lignin deposition in wheat stem. Waterlogging of wheat plants reduced internode lignin content, and this effect is accompanied by transcriptional repression of three of the genes characterized as highly expressed in wheat internode including phenylalanine ammonia-lyase6 (PAL6), CCR2 and F5H2, and decreased activity of PAL. Expression of the other genes was, however, induced by waterlogging, suggesting their role in the synthesis of other phenylpropanoid-derived molecules with roles in stress responses. Moreover, difference in internode lignin content between cultivars or change in its level due to waterlogging is associated with the level of cytokinin. CONCLUSION Lodging resistance, tolerance against biotic and abiotic stresses and feedstock quality of wheat biomass are closely associated with its lignin content. Therefore, the findings of this study provide important insights into the molecular mechanisms underlying lignin formation in wheat, an important step towards the development of molecular tools that can facilitate the breeding of wheat cultivars for optimized lignin content and enhanced feedstock quality without affecting other lignin-related agronomic benefits.
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Affiliation(s)
- Tran-Nguyen Nguyen
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, MB, R3T 2N2, Canada.
| | - SeungHyun Son
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, MB, R3T 2N2, Canada.
| | - Mark C Jordan
- Morden Reasearch and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada.
| | - David B Levin
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB, R3T 5V6, Canada.
| | - Belay T Ayele
- Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, MB, R3T 2N2, Canada.
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Jin X, Gou JY. A rapid and cost-effective fluorescence detection in tube (FDIT) method to analyze protein phosphorylation. PLANT METHODS 2016; 12:43. [PMID: 27822293 PMCID: PMC5094037 DOI: 10.1186/s13007-016-0143-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 10/17/2016] [Indexed: 05/12/2023]
Abstract
BACKGROUND Protein phosphorylation is one of the most important post-translational modifications catalyzed by protein kinases in living organisms. The advance of genome sequencing provided the information of protein kinase families in many organisms, including both model and non-model plants. The development of proteomics technologies also enabled scientists to efficiently reveal a large number of protein phosphorylations of an organism. However, kinases and phosphorylation targets are still to be connected to illustrate the complicated network in life. RESULTS Here we adapted Pro-Q® Diamond (Pro-Q® Diamond Phosphoprotein Gel Stain), a widely used phosphoprotein gel-staining fluorescence dye, to establish a rapid, economical and non-radioactive fluorescence detection in tube (FDIT) method to analyze phosphorylated proteins. Taking advantages of high sensitivity and specificity of Pro-Q® diamond, the FDIT method is also demonstrated to be rapid and reliable, with a suitable linear range for in vitro protein phosphorylation. A significant and satisfactory protein kinase reaction was detected as fast as 15 min from Wheat Kinase START 1.1 (WKS1.1) on a thylakoid ascorbate peroxidase (tAPX), an established phosphorylation target in our earlier study. CONCLUSION The FDIT method saves up to 95% of the dye consumed in a gel staining method. The FDIT method is remarkably quick, highly reproducible, unambiguous and capable to be scaled up to dozens of samples. The FDIT method could serve as a simple and sensitive alternative procedure to determine protein kinase reactions with zero radiation exposure, as a supplementation to other widely used radioactive and in-gel assays.
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Affiliation(s)
- Xiao Jin
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Jin-Ying Gou
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438 China
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Abstract
Rice is the most important staple food for a large part of the world's human population and also a key model organism for plant research. Here, we present Information Commons for Rice (IC4R; http://ic4r.org), a rice knowledgebase featuring adoption of an extensible and sustainable architecture that integrates multiple omics data through community-contributed modules. Each module is developed and maintained by different committed groups, deals with data collection, processing and visualization, and delivers data on-demand via web services. In the current version, IC4R incorporates a variety of rice data through multiple committed modules, including genome-wide expression profiles derived entirely from RNA-Seq data, resequencing-based genomic variations obtained from re-sequencing data of thousands of rice varieties, plant homologous genes covering multiple diverse plant species, post-translational modifications, rice-related literatures and gene annotations contributed by the rice research community. Unlike extant related databases, IC4R is designed for scalability and sustainability and thus also features collaborative integration of rice data and low costs for database update and maintenance. Future directions of IC4R include incorporation of other omics data and association of multiple omics data with agronomically important traits, dedicating to build IC4R into a valuable knowledgebase for both basic and translational researches in rice.
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Phosphorylation is an on/off switch for 5-hydroxyconiferaldehyde O-methyltransferase activity in poplar monolignol biosynthesis. Proc Natl Acad Sci U S A 2015; 112:8481-6. [PMID: 26109572 DOI: 10.1073/pnas.1510473112] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Although phosphorylation has long been known to be an important regulatory modification of proteins, no unequivocal evidence has been presented to show functional control by phosphorylation for the plant monolignol biosynthetic pathway. Here, we present the discovery of phosphorylation-mediated on/off regulation of enzyme activity for 5-hydroxyconiferaldehyde O-methyltransferase 2 (PtrAldOMT2), an enzyme central to monolignol biosynthesis for lignification in stem-differentiating xylem (SDX) of Populus trichocarpa. Phosphorylation turned off the PtrAldOMT2 activity, as demonstrated in vitro by using purified phosphorylated and unphosphorylated recombinant PtrAldOMT2. Protein extracts of P. trichocarpa SDX, which contains endogenous kinases, also phosphorylated recombinant PtrAldOMT2 and turned off the recombinant protein activity. Similarly, ATP/Mn(2+)-activated phosphorylation of SDX protein extracts reduced the endogenous SDX PtrAldOMT2 activity by ∼ 60%, and dephosphorylation fully restored the activity. Global shotgun proteomic analysis of phosphopeptide-enriched P. trichocarpa SDX protein fractions identified PtrAldOMT2 monophosphorylation at Ser(123) or Ser(125) in vivo. Phosphorylation-site mutagenesis verified the PtrAldOMT2 phosphorylation at Ser(123) or Ser(125) and confirmed the functional importance of these phosphorylation sites for O-methyltransferase activity. The PtrAldOMT2 Ser(123) phosphorylation site is conserved across 93% of AldOMTs from 46 diverse plant species, and 98% of the AldOMTs have either Ser(123) or Ser(125). PtrAldOMT2 is a homodimeric cytosolic enzyme expressed more abundantly in syringyl lignin-rich fiber cells than in guaiacyl lignin-rich vessel cells. The reversible phosphorylation of PtrAldOMT2 is likely to have an important role in regulating syringyl monolignol biosynthesis of P. trichocarpa.
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Mitra SK, Chen R, Dhandaydham M, Wang X, Blackburn RK, Kota U, Goshe MB, Schwartz D, Huber SC, Clouse SD. An autophosphorylation site database for leucine-rich repeat receptor-like kinases in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:1042-1060. [PMID: 25912465 DOI: 10.1111/tpj.12863] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 04/21/2015] [Indexed: 06/04/2023]
Abstract
Leucine-rich repeat receptor-like kinases (LRR RLKs) form a large family of plant signaling proteins consisting of an extracellular domain connected by a single-pass transmembrane sequence to a cytoplasmic kinase domain. Autophosphorylation on specific Ser and/or Thr residues in the cytoplasmic domain is often critical for the activation of several LRR RLK family members with proven functional roles in plant growth regulation, morphogenesis, disease resistance, and stress responses. While identification and functional characterization of in vivo phosphorylation sites is ultimately required for a full understanding of LRR RLK biology and function, bacterial expression of recombinant LRR RLK cytoplasmic catalytic domains for identification of in vitro autophosphorylation sites provides a useful resource for further targeted identification and functional analysis of in vivo sites. In this study we employed high-throughput cloning and a variety of mass spectrometry approaches to generate an autophosphorylation site database representative of more than 30% of the approximately 223 LRR RLKs in Arabidopsis thaliana. We used His-tagged constructs of complete cytoplasmic domains to identify a total of 592 phosphorylation events across 73 LRR RLKs, with 497 sites uniquely assigned to specific Ser (268 sites) or Thr (229 sites) residues in 68 LRR RLKs. Multiple autophosphorylation sites per LRR RLK were the norm, with an average of seven sites per cytoplasmic domain, while some proteins showed more than 20 unique autophosphorylation sites. The database was used to analyze trends in the localization of phosphorylation sites across cytoplasmic kinase subdomains and to derive a statistically significant sequence motif for phospho-Ser autophosphorylation.
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Affiliation(s)
- Srijeet K Mitra
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - Ruiqiang Chen
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - Murali Dhandaydham
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - Xiaofeng Wang
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - Robert Kevin Blackburn
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Uma Kota
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Michael B Goshe
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Daniel Schwartz
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, 06269, USA
| | - Steven C Huber
- USDA/ARS, University of Illinois, Urbana, IL, 61801, USA
| | - Steven D Clouse
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27695, USA
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