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Sathapondecha P, Suksri P, Nuanpirom J, Nakkanong K, Nualsri C, Whankaew S. Development of Gene-Based InDel Markers on Putative Drought Stress-Responsive Genes and Genetic Diversity of Durian (Durio zibethinus). Biochem Genet 2024:10.1007/s10528-023-10638-9. [PMID: 38306004 DOI: 10.1007/s10528-023-10638-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 12/12/2023] [Indexed: 02/03/2024]
Abstract
Insertion-deletion (InDel) markers are co-dominant, relatively abundant and practical for agarose gel genotyping. InDel polymorphism usually affects gene functions. Nucleotide sequences of durian (Durio zibethinus) are available, but InDel makers have not been well established. This study aimed to develop drought-related gene-based InDel markers for durian through bioinformatic analysis of RNA-Seq datasets. The polymorphism of the markers was verified in 24 durian genotypes local to Thailand. Bioinformatic analysis indicated 496 InDel loci having lengths more than 9 bp. To evaluate these InDel markers, 15 InDel loci were selected. Nine markers were successfully amplified a clear polymorphic band pattern on 2% agarose gel. The polymorphic information content (PIC) of these nine markers ranged from 0.1103 to 0.5808. The genetic distance between the 24 genotypes ranged from 0.222 to 0.889. The phylogeny based on the nine InDel loci distinguished the 24 genotypes and divided samples into four groups. This set of gene-based InDel markers on putative drought-responsive genes will be useful for genetic studies.
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Affiliation(s)
- Ponsit Sathapondecha
- Center for Genomics and Bioinformatics Research, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Phassorn Suksri
- Center for Genomics and Bioinformatics Research, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Jiratchaya Nuanpirom
- Center for Genomics and Bioinformatics Research, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Korakot Nakkanong
- Department of Plant Science, Faculty of Natural Resources, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
- Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok, 10900, Thailand
| | - Charassri Nualsri
- Department of Plant Science, Faculty of Natural Resources, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
- Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok, 10900, Thailand
| | - Sukhuman Whankaew
- Department of Plant Science, Faculty of Technology and Community Development, Thaksin University, Phatthalung Campus, Phatthalung, 93210, Thailand.
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Madison I, Amin F, Song K, Sozzani R, Van den Broeck L. A Data-Driven Signaling Network Inference Approach for Phosphoproteomics. Methods Mol Biol 2023; 2690:335-354. [PMID: 37450158 DOI: 10.1007/978-1-0716-3327-4_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Proteins are rapidly and dynamically post-transcriptionally modified as cells respond to changes in their environment. For example, protein phosphorylation is mediated by kinases while dephosphorylation is mediated by phosphatases. Quantifying and predicting interactions between kinases, phosphatases, and target proteins over time will aid the study of signaling cascades under a variety of environmental conditions. Here, we describe methods to statistically analyze label-free phosphoproteomic data and infer posttranscriptional regulatory networks over time. We provide an R-based method that can be used to normalize and analyze label-free phosphoproteomic data using variance stabilizing normalization and a linear mixed model across multiple time points and conditions. We also provide a method to infer regulator-target interactions over time using a discretization scheme followed by dynamic Bayesian modeling computations to validate our conclusions. Overall, this pipeline is designed to perform functional analyses and predictions of phosphoproteomic signaling cascades.
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Affiliation(s)
- Imani Madison
- Department of Plant and Microbial Biology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC, USA
| | - Fin Amin
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, USA
| | - Kuncheng Song
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC, USA.
| | - Lisa Van den Broeck
- Department of Plant and Microbial Biology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC, USA.
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Materials, workflows and applications of IMAC for phosphoproteome profiling in the recent decade: A review. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Jiang W, He P, Zhou M, Lu X, Chen K, Liang C, Tian J. Soybean responds to phosphate starvation through reversible protein phosphorylation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:222-234. [PMID: 34371392 DOI: 10.1016/j.plaphy.2021.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/19/2021] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
Phosphorus (P) deficiency is considered as a major constraint on crop production. Although a set of adaptative strategies are extensively suggested in soybean (Glycine max) to phosphate (Pi) deprivation, molecular mechanisms underlying reversible protein phosphorylation in soybean responses to P deficiency remains largely unclear. In this study, isobaric tags for relative and absolute quantitation, combined with liquid chromatography and tandem mass spectrometry analysis was performed to identify differential phosphoproteins in soybean roots under Pi sufficient and deficient conditions. A total of 427 phosphoproteins were found to exhibit differential accumulations, with 213 up-regulated and 214 down-regulated. Among them, a nitrate reductase, GmNR4 exhibiting increased phosphorylation levels under low Pi conditions, was further selected to evaluate the effects of phosphorylation on its nitrate reductase activity and subcellular localization. Mutations of GmNR4 phosphorylation levels significantly influenced its activity in vitro, but not for its subcellular localization. Taken together, identification of differential phosphoproteins reveled the complex regulatory pathways for soybean adaptation to Pi starvation through reversible protein phosphorylation.
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Affiliation(s)
- Weizhen Jiang
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China; School of Traditional Chinese Medicine Resources, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Panmin He
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Ming Zhou
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Xing Lu
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Kang Chen
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Cuiyue Liang
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China.
| | - Jiang Tian
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China.
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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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O'Leary B, Plaxton WC. Multifaceted functions of post-translational enzyme modifications in the control of plant glycolysis. CURRENT OPINION IN PLANT BIOLOGY 2020; 55:28-37. [PMID: 32200227 DOI: 10.1016/j.pbi.2020.01.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/24/2020] [Accepted: 01/31/2020] [Indexed: 06/10/2023]
Abstract
Glycolysis is a central feature of metabolism and its regulation plays important roles during plant developmental and stress responses. Recent advances in proteomics and mass spectrometry have documented extensive and dynamic post-translational modifications (PTMs) of most glycolytic enzymes in diverse plant tissues. Protein PTMs represent fundamental regulatory events that integrate signalling and gene expression with cellular metabolic networks, and can regulate glycolytic enzyme activity, localization, protein:protein interactions, moonlighting functions, and turnover. Serine/threonine phosphorylation and redox PTMs of cysteine thiol groups appear to be the most prevalent forms of reversible covalent modification involved in plant glycolytic control. Additional PTMs including monoubiquitination also have important functions. However, the molecular functions and mechanisms of most glycolytic enzyme PTMs remain unknown, and represent important objectives for future studies.
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Affiliation(s)
- Brendan O'Leary
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Australia
| | - William C Plaxton
- Department of Biology, Queen's University, Kingston, Ontario K7L3N6, Canada.
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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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Wang X, Xu C, Cai X, Wang Q, Dai S. Heat-Responsive Photosynthetic and Signaling Pathways in Plants: Insight from Proteomics. Int J Mol Sci 2017; 18:E2191. [PMID: 29053587 PMCID: PMC5666872 DOI: 10.3390/ijms18102191] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/13/2017] [Accepted: 10/16/2017] [Indexed: 02/04/2023] Open
Abstract
Heat stress is a major abiotic stress posing a serious threat to plants. Heat-responsive mechanisms in plants are complicated and fine-tuned. Heat signaling transduction and photosynthesis are highly sensitive. Therefore, a thorough understanding of the molecular mechanism in heat stressed-signaling transduction and photosynthesis is necessary to protect crop yield. Current high-throughput proteomics investigations provide more useful information for underlying heat-responsive signaling pathways and photosynthesis modulation in plants. Several signaling components, such as guanosine triphosphate (GTP)-binding protein, nucleoside diphosphate kinase, annexin, and brassinosteroid-insensitive I-kinase domain interacting protein 114, were proposed to be important in heat signaling transduction. Moreover, diverse protein patterns of photosynthetic proteins imply that the modulations of stomatal CO₂ exchange, photosystem II, Calvin cycle, ATP synthesis, and chlorophyll biosynthesis are crucial for plant heat tolerance.
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Affiliation(s)
- Xiaoli Wang
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Chenxi Xu
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Xiaofeng Cai
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Quanhua Wang
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Shaojun Dai
- Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China.
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