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Ren H, Ou Q, Pu Q, Lou Y, Yang X, Han Y, Liu S. Comprehensive Review on Bimolecular Fluorescence Complementation and Its Application in Deciphering Protein-Protein Interactions in Cell Signaling Pathways. Biomolecules 2024; 14:859. [PMID: 39062573 PMCID: PMC11274695 DOI: 10.3390/biom14070859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/14/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Signaling pathways are responsible for transmitting information between cells and regulating cell growth, differentiation, and death. Proteins in cells form complexes by interacting with each other through specific structural domains, playing a crucial role in various biological functions and cell signaling pathways. Protein-protein interactions (PPIs) within cell signaling pathways are essential for signal transmission and regulation. The spatiotemporal features of PPIs in signaling pathways are crucial for comprehending the regulatory mechanisms of signal transduction. Bimolecular fluorescence complementation (BiFC) is one kind of imaging tool for the direct visualization of PPIs in living cells and has been widely utilized to uncover novel PPIs in various organisms. BiFC demonstrates significant potential for application in various areas of biological research, drug development, disease diagnosis and treatment, and other related fields. This review systematically summarizes and analyzes the technical advancement of BiFC and its utilization in elucidating PPIs within established cell signaling pathways, including TOR, PI3K/Akt, Wnt/β-catenin, NF-κB, and MAPK. Additionally, it explores the application of this technology in revealing PPIs within the plant hormone signaling pathways of ethylene, auxin, Gibberellin, and abscisic acid. Using BiFC in conjunction with CRISPR-Cas9, live-cell imaging, and ultra-high-resolution microscopy will enhance our comprehension of PPIs in cell signaling pathways.
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Affiliation(s)
| | | | | | | | | | | | - Shiping Liu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400716, China; (H.R.); (Q.O.); (Q.P.); (Y.L.); (X.Y.); (Y.H.)
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Liu M, Ma L, Tang Y, Yang W, Yang Y, Xi J, Wang X, Zhu W, Xue J, Zhang X, Xu S. Maize Autophagy-Related Protein ZmATG3 Confers Tolerance to Multiple Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2024; 13:1637. [PMID: 38931070 PMCID: PMC11207562 DOI: 10.3390/plants13121637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/05/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024]
Abstract
Abiotic stresses pose a major increasing problem for the cultivation of maize. Autophagy plays a vital role in recycling and re-utilizing nutrients and adapting to stress. However, the role of autophagy in the response to abiotic stress in maize has not yet been investigated. Here, ZmATG3, which is essential for ATG8-PE conjugation, was isolated from the maize inbred line B73. The ATG3 sequence was conserved, including the C-terminal domains with HPC and FLKF motifs and the catalytic domain in different species. The promoter of the ZmATG3 gene contained a number of elements involved in responses to environmental stresses or hormones. Heterologous expression of ZmATG3 in yeast promoted the growth of strain under salt, mannitol, and low-nitrogen stress. The expression of ZmATG3 could be altered by various types of abiotic stress (200 mM NaCl, 200 mM mannitol, low N) and exogenous hormones (500 µM ABA). GUS staining analysis of ZmATG3-GUS transgenic Arabidopsis revealed that GUS gene activity increased after abiotic treatment. ZmATG3-overexpressing Arabidopsis plants had higher osmotic and salinity stress tolerance than wild-type plants. Overexpression of ZmATG3 up-regulated the expression of other AtATGs (AtATG3, AtATG5, and AtATG8b) under NaCl, mannitol and LN stress. These findings demonstrate that overexpression of ZmATG3 can improve tolerance to multiple abiotic stresses.
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Affiliation(s)
- Mengli Liu
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China; (M.L.); (L.M.); (Y.T.); (W.Y.); (Y.Y.); (J.X.); (W.Z.); (J.X.)
| | - Li Ma
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China; (M.L.); (L.M.); (Y.T.); (W.Y.); (Y.Y.); (J.X.); (W.Z.); (J.X.)
| | - Yao Tang
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China; (M.L.); (L.M.); (Y.T.); (W.Y.); (Y.Y.); (J.X.); (W.Z.); (J.X.)
| | - Wangjin Yang
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China; (M.L.); (L.M.); (Y.T.); (W.Y.); (Y.Y.); (J.X.); (W.Z.); (J.X.)
| | - Yuyin Yang
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China; (M.L.); (L.M.); (Y.T.); (W.Y.); (Y.Y.); (J.X.); (W.Z.); (J.X.)
| | - Jing Xi
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China; (M.L.); (L.M.); (Y.T.); (W.Y.); (Y.Y.); (J.X.); (W.Z.); (J.X.)
| | - Xuan Wang
- Yangling Qinfeng Seed-Industry Co., Ltd., Yangling 712100, China;
| | - Wanchao Zhu
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China; (M.L.); (L.M.); (Y.T.); (W.Y.); (Y.Y.); (J.X.); (W.Z.); (J.X.)
| | - Jiquan Xue
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China; (M.L.); (L.M.); (Y.T.); (W.Y.); (Y.Y.); (J.X.); (W.Z.); (J.X.)
| | - Xinghua Zhang
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China; (M.L.); (L.M.); (Y.T.); (W.Y.); (Y.Y.); (J.X.); (W.Z.); (J.X.)
| | - Shutu Xu
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China; (M.L.); (L.M.); (Y.T.); (W.Y.); (Y.Y.); (J.X.); (W.Z.); (J.X.)
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3
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Zhou H, Huo Y, Yang N, Wei T. Phosphatidic acid: from biophysical properties to diverse functions. FEBS J 2024; 291:1870-1885. [PMID: 37103336 DOI: 10.1111/febs.16809] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 03/15/2023] [Accepted: 04/26/2023] [Indexed: 04/28/2023]
Abstract
Phosphatidic acid (PA), the simplest phospholipid, acts as a key metabolic intermediate and second messenger that impacts diverse cellular and physiological processes across species ranging from microbes to plants and mammals. The cellular levels of PA dynamically change in response to stimuli, and multiple enzymatic reactions can mediate its production and degradation. PA acts as a signalling molecule and regulates various cellular processes via its effects on membrane tethering, enzymatic activities of target proteins, and vesicular trafficking. Because of its unique physicochemical properties compared to other phospholipids, PA has emerged as a class of new lipid mediators influencing membrane structure, dynamics, and protein interactions. This review summarizes the biosynthesis, dynamics, and cellular functions and properties of PA.
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Affiliation(s)
- Hejiang Zhou
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yanwu Huo
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Na Yang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Laboratory of Genetic and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Taotao Wei
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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Qi F, Li J, Ai Y, Shangguan K, Li P, Lin F, Liang Y. DGK5β-derived phosphatidic acid regulates ROS production in plant immunity by stabilizing NADPH oxidase. Cell Host Microbe 2024; 32:425-440.e7. [PMID: 38309260 DOI: 10.1016/j.chom.2024.01.011] [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] [Received: 09/12/2023] [Revised: 12/20/2023] [Accepted: 01/23/2024] [Indexed: 02/05/2024]
Abstract
In plant immunity, phosphatidic acid (PA) regulates reactive oxygen species (ROS) by binding to respiratory burst oxidase homolog D (RBOHD), an NADPH oxidase responsible for ROS production. Here, we analyze the influence of PA binding on RBOHD activity and the mechanism of RBOHD-bound PA generation. PA binding enhances RBOHD protein stability by inhibiting vacuolar degradation, thereby increasing chitin-induced ROS production. Mutations in diacylglycerol kinase 5 (DGK5), which phosphorylates diacylglycerol to produce PA, impair chitin-induced PA and ROS production. The DGK5 transcript DGK5β (but not DGK5α) complements reduced PA and ROS production in dgk5-1 mutants, as well as resistance to Botrytis cinerea. Phosphorylation of S506 residue in the C-terminal calmodulin-binding domain of DGK5β contributes to the activation of DGK5β to produce PA. These findings suggest that DGK5β-derived PA regulates ROS production by inhibiting RBOHD protein degradation, elucidating the role of PA-ROS interplay in immune response regulation.
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Affiliation(s)
- Fan Qi
- Zhejiang Xianghu Laboratory, Department of Plant Protection, Zhejiang University, Hangzhou 310058, China
| | - Jianwei Li
- Zhejiang Xianghu Laboratory, Department of Plant Protection, Zhejiang University, Hangzhou 310058, China
| | - Yingfei Ai
- Zhejiang Xianghu Laboratory, Department of Plant Protection, Zhejiang University, Hangzhou 310058, China
| | - Keke Shangguan
- Zhejiang Xianghu Laboratory, Department of Plant Protection, Zhejiang University, Hangzhou 310058, China
| | - Ping Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Hangzhou 311200, China
| | - Fucheng Lin
- Zhejiang Xianghu Laboratory, Department of Plant Protection, Zhejiang University, Hangzhou 310058, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Hangzhou 311200, China.
| | - Yan Liang
- Zhejiang Xianghu Laboratory, Department of Plant Protection, Zhejiang University, Hangzhou 310058, China.
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Bao HN, Yin J, Wang LY, Wang RH, Huang LQ, Chen YL, Wu JX, Sun JQ, Liu WW, Yao N, Li J. Aberrant accumulation of ceramides in mitochondria triggers cell death by inducing autophagy in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1314-1330. [PMID: 38069660 DOI: 10.1093/jxb/erad456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/05/2023] [Indexed: 02/29/2024]
Abstract
Sphingolipids are membrane lipids and play critical roles in signal transduction. Ceramides are central components of sphingolipid metabolism that are involved in cell death. However, the mechanism of ceramides regulating cell death in plants remains unclear. Here, we found that ceramides accumulated in mitochondria of accelerated cell death 5 mutant (acd5), and expression of mitochondrion-localized ceramide kinase (ACD5) suppressed mitochondrial ceramide accumulation and the acd5 cell death phenotype. Using immuno-electron microscopy, we observed hyperaccumulation of ceramides in acer acd5 double mutants, which are characterized by mutations in both ACER (alkaline ceramidase) and ACD5 genes. The results confirmed that plants with specific ceramide accumulation exhibited localization of ceramides to mitochondria, resulting in an increase in mitochondrial reactive oxygen species production. Interestingly, when compared with the wild type, autophagy-deficient mutants showed stronger resistance to ceramide-induced cell death. Lipid profiling analysis demonstrated that plants with ceramide accumulation exhibited a significant increase in phosphatidylethanolamine levels. Furthermore, exogenous ceramide treatment or endogenous ceramide accumulation induces autophagy. When exposed to exogenous ceramides, an increase in the level of the autophagy-specific ubiquitin-like protein, ATG8e, associated with mitochondria, where it directly bound to ceramides. Taken together, we propose that the accumulation of ceramides in mitochondria can induce cell death by regulating autophagy.
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Affiliation(s)
- He-Nan Bao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Jian Yin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
- College of JunCao Science and Ecology and Center for Horticultural Biology and Metabolomics, Fujian Agriculture and Forestry University, Fuzhou, Fujian, P. R. China
| | - Ling-Yan Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Rui-Hua Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Li-Qun Huang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Yi-Li Chen
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Jian-Xin Wu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Jia-Qi Sun
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Wei-Wei Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Nan Yao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
| | - Jian Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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Werelusz P, Galiniak S, Mołoń M. Molecular functions of moonlighting proteins in cell metabolic processes. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119598. [PMID: 37774631 DOI: 10.1016/j.bbamcr.2023.119598] [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: 01/25/2023] [Revised: 09/10/2023] [Accepted: 09/17/2023] [Indexed: 10/01/2023]
Abstract
Moonlighting proteins have more than one physiologically significant role within one polypeptide chain. The multifunctionality of proteins was first described in 1987 by Joram Piatigorsky and Graeme Wistow. Cells can benefit from involvement of these proteins in biological processes in several ways, e.g. at the energy level. Furthermore, cells have developed a number of mechanisms to change these proteins' functions. Moonlighting proteins are found in all types of organisms, including prokaryotes, eukaryotes, and even viruses. These proteins include a variety of enzymes that serve as receptors, secreted cytokines, transcription factors, or proteasome components. Additionally, there are many combinations of functions, e.g. among receptors and transcription factors, chaperones and cytokines, as well as transcription factors within the ribosome. This work describes enzymes involved in several important metabolic processes in cells, namely cellular respiration, gluconeogenesis, the urea cycle, and pentose phosphate metabolism.
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Affiliation(s)
| | - Sabina Galiniak
- Institute of Medical Sciences, Rzeszów University, Rzeszów, Poland
| | - Mateusz Mołoń
- Institute of Biology, Rzeszów University, Rzeszów, Poland.
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Jiang YT, Yang LH, Zheng JX, Geng XC, Bai YX, Wang YC, Xue HW, Lin WH. Vacuolar H +-ATPase and BZR1 form a feedback loop to regulate the homeostasis of BR signaling in Arabidopsis. MOLECULAR PLANT 2023; 16:1976-1989. [PMID: 37837193 DOI: 10.1016/j.molp.2023.10.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 09/29/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
Abstract
Brassinosteroid (BR) is a vital plant hormone that regulates plant growth and development. BRASSINAZOLE RESISTANT 1 (BZR1) is a key transcription factor in BR signaling, and its nucleocytoplasmic localization is crucial for BR signaling. However, the mechanisms that regulate BZR1 nucleocytoplasmic distribution and thus the homeostasis of BR signaling remain largely unclear. The vacuole is the largest organelle in mature plant cells and plays a key role in maintenance of cellular pH, storage of intracellular substances, and transport of ions. In this study, we uncovered a novel mechanism of BR signaling homeostasis regulated by the vacuolar H+-ATPase (V-ATPase) and BZR1 feedback loop. Our results revealed that the vha-a2 vha-a3 mutant (vha2, lacking V-ATPase activity) exhibits enhanced BR signaling with increased total amount of BZR1, nuclear-localized BZR1, and the ratio of BZR1/phosphorylated BZR1 in the nucleus. Further biochemical assays revealed that VHA-a2 and VHA-a3 of V-ATPase interact with the BZR1 protein through a domain that is conserved across multiple species. VHA-a2 and VHA-a3 negatively regulate BR signaling by interacting with BZR1 and promoting its retention in the tonoplast. Interestingly, a series of molecular analyses demonstrated that nuclear-localized BZR1 could bind directly to specific motifs in the promoters of VHA-a2 and VHA-a3 to promote their expression. Taken together, these results suggest that V-ATPase and BZR1 may form a feedback regulatory loop to maintain the homeostasis of BR signaling in Arabidopsis, providing new insights into vacuole-mediated regulation of hormone signaling.
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Affiliation(s)
- Yu-Tong Jiang
- School of Life Sciences and Biotechnology, The Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, Shanghai 200240, China; School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lu-Han Yang
- School of Life Sciences and Biotechnology, The Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ji-Xuan Zheng
- Zhiyuan College, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xian-Chen Geng
- School of Life Sciences and Biotechnology, The Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yu-Xuan Bai
- Zhiyuan College, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yu-Chen Wang
- Zhiyuan College, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hong-Wei Xue
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, Shanghai 200240, China; School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wen-Hui Lin
- School of Life Sciences and Biotechnology, The Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, Shanghai 200240, China.
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Ma X, Feng L, Tao A, Zenda T, He Y, Zhang D, Duan H, Tao Y. Identification and validation of seed dormancy loci and candidate genes and construction of regulatory networks by WGCNA in maize introgression lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:259. [PMID: 38038768 DOI: 10.1007/s00122-023-04495-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/26/2023] [Indexed: 12/02/2023]
Abstract
KEY MESSAGE Seventeen PHS-QTLs and candidate genes were obtained, including eleven major loci, three under multiple environments and two with co-localization by the other mapping methods; The functions of three candidate genes were validated using mutants; nine target proteins and five networks were filtered by joint analysis of GWAS and WGCNA. Seed dormancy (SD) and pre-harvest sprouting (PHS) affect yield, as well as grain and hybrid quality in seed production. Therefore, identification of genetic and regulatory pathways underlying PHS and SD is key to gene function analysis, allelic variation mining and genetic improvement. In this study, 78,360 SNPs by SLAF-seq of 230 maize chromosome segment introgression lines (ILs), PHS under five environments were used to conduct GWAS (genome wide association study) (a threshold of 1/n), and seventeen unreported PHS QTLs were obtained, including eleven QTLs with PVE > 10% and three QTLs under multiple environments. Two QTL loci were co-located between the other two genetic mapping methods. Using differential gene expression analyses at two stages of grain development, gene functional analysis of Arabidopsis mutants, and gene functional analysis in the QTL region, seventeen PHS QTL-linked candidate genes were identified, and their five molecular regulatory networks constructed. Based on the Arabidopsis T-DNA mutations, three candidate genes were shown to regulate for SD and PHS. Meanwhile, using RNA-seq of grain development, the weighted correlation network analysis (WGCNA) was performed, deducing five regulatory pathways and target genes that regulate PHS and SD. Based on the conjoint analysis of GWAS and WGCNA, four pathways, nine target proteins and target genes were revealed, most of which regulate cell wall metabolism, cell proliferation and seed dehydration tolerance. This has important theoretical and practical significance for elucidating the genetic basis of maize PHS and SD, as well as mining of genetic resources and genetic improvement of traits.
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Affiliation(s)
- Xiaolin Ma
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Liqing Feng
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Anyan Tao
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Tinashe Zenda
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Yuan He
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Daxiao Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Huijun Duan
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.
| | - Yongsheng Tao
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.
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Pan T, Liu Y, Hu X, Li P, Lin C, Tang Y, Tang W, Liu Y, Guo L, Kim C, Fang J, Lin H, Wu Z, Blumwald E, Wang S. Stress-induced endocytosis from chloroplast inner envelope membrane is mediated by CHLOROPLAST VESICULATION but inhibited by GAPC. Cell Rep 2023; 42:113208. [PMID: 37792531 DOI: 10.1016/j.celrep.2023.113208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 06/16/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023] Open
Abstract
Clathrin-mediated vesicular formation and trafficking are responsible for molecular cargo transport and signal transduction among organelles. Our previous study shows that CHLOROPLAST VESICULATION (CV)-containing vesicles (CVVs) are generated from chloroplasts for chloroplast degradation under abiotic stress. Here, we show that CV interacts with the clathrin heavy chain (CHC) and induces vesicle budding toward the cytosol from the chloroplast inner envelope membrane. In the defective mutants of CHC2 and the dynamin-encoding DRP1A, CVV budding and releasing from chloroplast are impeded. The mutations of CHC2 inhibit CV-induced chloroplast degradation and hypersensitivity to water stress. Moreover, CV-CHC2 interaction is impaired by the oxidized GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (GAPC). GAPC1 overexpression suppresses CV-mediated chloroplast degradation and hypersensitivity to water stress, while CV silencing alleviates the hypersensitivity of the gapc1gapc2 plant to water stress. Together, our work identifies a pathway of clathrin-assisted CVV budding outward from chloroplast, which is involved in chloroplast degradation and stress response.
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Affiliation(s)
- Ting Pan
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei 230036, China; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yangxuan Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Xufan Hu
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Pengwei Li
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Chengcheng Lin
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Yuying Tang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Wei Tang
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Yongsheng Liu
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Chanhong Kim
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jun Fang
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Honghui Lin
- Ministry of Education, Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Zhihua Wu
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Songhu Wang
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei 230036, China; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
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10
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Lee DH, Choi I, Park SJ, Kim S, Choi MS, Lee HS, Pai HS. Three consecutive cytosolic glycolysis enzymes modulate autophagic flux. PLANT PHYSIOLOGY 2023; 193:1797-1815. [PMID: 37539947 PMCID: PMC10602606 DOI: 10.1093/plphys/kiad439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 05/25/2023] [Accepted: 06/19/2023] [Indexed: 08/05/2023]
Abstract
Autophagy serves as an important recycling route for the growth and survival of eukaryotic organisms in nutrient-deficient conditions. Since starvation induces massive changes in the metabolic flux that are coordinated by key metabolic enzymes, specific processing steps of autophagy may be linked with metabolic flux-monitoring enzymes. We attempted to identify carbon metabolic genes that modulate autophagy using VIGS screening of 45 glycolysis- and Calvin-Benson cycle-related genes in Arabidopsis (Arabidopsis thaliana). Here, we report that three consecutive triose-phosphate-processing enzymes involved in cytosolic glycolysis, triose-phosphate-isomerase (TPI), glyceraldehyde-3-phosphate dehydrogenase (GAPC), and phosphoglycerate kinase (PGK), designated TGP, negatively regulate autophagy. Depletion of TGP enzymes causes spontaneous autophagy induction and increases AUTOPHAGY-RELATED 1 (ATG1) kinase activity. TGP enzymes interact with ATG101, a regulatory component of the ATG1 kinase complex. Spontaneous autophagy induction and abnormal growth under insufficient sugar in TGP mutants are suppressed by crossing with the atg101 mutant. Considering that triose-phosphates are photosynthates transported to the cytosol from active chloroplasts, the TGP enzymes would be strategically positioned to monitor the flow of photosynthetic sugars and modulate autophagy accordingly. Collectively, these results suggest that TGP enzymes negatively control autophagy acting upstream of the ATG1 complex, which is critical for seedling development.
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Affiliation(s)
- Du-Hwa Lee
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
- Department of Systems Biology, Yonsei University, Seoul 03722, Korea
| | - Ilyeong Choi
- Department of Systems Biology, Yonsei University, Seoul 03722, Korea
| | - Seung Jun Park
- Department of Systems Biology, Yonsei University, Seoul 03722, Korea
| | - Sumin Kim
- Department of Systems Biology, Yonsei University, Seoul 03722, Korea
| | - Min-Soo Choi
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Ho-Seok Lee
- Department of Biology, Kyung Hee University, Seoul 02447, Korea
- Center for Genome Engineering, Institute for Basic Science, Daejeon 34126, Korea
| | - Hyun-Sook Pai
- Department of Systems Biology, Yonsei University, Seoul 03722, Korea
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11
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Liu X, Tian J, Liu G, Sun L. Multi-Omics Analysis Reveals Mechanisms of Strong Phosphorus Adaptation in Tea Plant Roots. Int J Mol Sci 2023; 24:12431. [PMID: 37569806 PMCID: PMC10419353 DOI: 10.3390/ijms241512431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/14/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023] Open
Abstract
Low phosphorus (P) is a major limiting factor for plant growth in acid soils, which are preferred by tea plants. This study aims to investigate the unique mechanisms of tea plant roots adaptation to low-P conditions. Tea plant roots were harvested for multi-omics analysis after being treated with 0 µmol·L-1 P (0P) and 250 µmol·L-1 P (250P) for 30 days. Under 250P conditions, root elongation was significantly inhibited, and the density of lateral roots was dramatically increased. This suggests that 250P may inhibit the elongation of tea plant roots. Moreover, the P concentration in roots was about 4.58 times higher than that under 0P, indicating that 250P may cause P toxicity in tea plant roots. Contrary to common plants, the expression of CsPT1/2 in tea plant roots was significantly increased by four times at 250P, which indicated that tea plant roots suffering from P toxicity might be due to the excessive expression of phosphate uptake-responsible genes under 250P conditions. Additionally, 94.80% of P-containing metabolites accumulated due to 250P stimulation, most of which were energy-associated metabolites, including lipids, nucleotides, and sugars. Especially the ratio of AMP/ATP and the expression of energy sensor CsSnRKs were inhibited by P application. Therefore, under 250P conditions, P over-accumulation due to the excessive expression of CsPT1/2 may inhibit energy metabolism and thus the growth of tea plant roots.
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Affiliation(s)
- Xiaomei Liu
- College of Tropical Crops, Hainan University, Haikou 570228, China;
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
- Institute of Tropical Crops Genetic Resources, Chinese Academy of Tropical Agriculture Sciences, Haikou 570228, China;
| | - Jing Tian
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Guodao Liu
- Institute of Tropical Crops Genetic Resources, Chinese Academy of Tropical Agriculture Sciences, Haikou 570228, China;
| | - Lili Sun
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
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12
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Chen XW, Zheng YY, Ouyang JM. Sulfated Undaria pinnatifida Polysaccharide Promotes Endocytosis of Nano-Calcium Oxalate Dihydrate by Repairing Subcellular Organelles in HK-2 Cells. Antioxidants (Basel) 2023; 12:antiox12051015. [PMID: 37237881 DOI: 10.3390/antiox12051015] [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: 02/21/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
The clinical manifestation of primary hyperoxaluria includes hyperoxaluria and recurrent urinary calculi. In this study, an oxidative damage model was constructed based on oxalate damage to the human renal proximal tubular epithelial cells (HK-2), and a comparative study was carried out on four different sulfated levels of Undaria pinnatifida polysaccharides (UPP0, UPP1, UPP2, and UPP3 with sulfate group [-OSO3-] contents of 1.59%, 6.03%, 20.83%, and 36.39%, respectively) on the repair of oxidatively damaged HK-2 cells. The results showed that after repair by UPPs, cell viability was enhanced, healing ability was improved, the intracellular superoxide dismutase level and mitochondrial membrane potential were increased, malondialdehyde, reactive oxygen species, and intracellular Ca2+ levels were reduced, cellular autophagy was reduced; lysosomal integrity was improved, and cytoskeleton and cell morphology were restored. The ability of repaired cells to endocytose nano-calcium oxalate dihydrate crystals (nano-COD) was enhanced. The activity of UPPs was closely related to their -OSO3- content. A too high or too low -OSO3- content was not conducive to polysaccharide activity, and only UPP2 exhibited the best cell repair ability and strongest ability to promote the cell endocytosis of crystals. UPP2 may be used as a potential agent to inhibit CaOx crystal deposition caused by high oxalate concentration.
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Affiliation(s)
- Xue-Wu Chen
- Institute of Biomineralization and Lithiasis Research, College of Chemistry and Materials Science, Jinan University, Guangzhou 510632, China
| | - Yu-Yun Zheng
- Institute of Biomineralization and Lithiasis Research, College of Chemistry and Materials Science, Jinan University, Guangzhou 510632, China
| | - Jian-Ming Ouyang
- Institute of Biomineralization and Lithiasis Research, College of Chemistry and Materials Science, Jinan University, Guangzhou 510632, China
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13
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Zhao W, Wang L, Li L, Zhou T, Yan F, Zhang H, Zhu Y, Andika IB, Sun L. Coat protein of rice stripe virus enhances autophagy activity through interaction with cytosolic glyceraldehyde-3-phosphate dehydrogenases, a negative regulator of plant autophagy. STRESS BIOLOGY 2023; 3:3. [PMID: 37676568 PMCID: PMC10441990 DOI: 10.1007/s44154-023-00084-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/28/2023] [Indexed: 09/08/2023]
Abstract
Viral infection commonly induces autophagy, leading to antiviral responses or conversely, promoting viral infection or replication. In this study, using the experimental plant Nicotiana benthamiana, we demonstrated that the rice stripe virus (RSV) coat protein (CP) enhanced autophagic activity through interaction with cytosolic glyceraldehyde-3-phosphate dehydrogenase 2 (GAPC2), a negative regulator of plant autophagy that binds to an autophagy key factor, autophagy-related protein 3 (ATG3). Competitive pull-down and co-immunoprecipitation (Co-IP)assays showed that RSV CP activated autophagy by disrupting the interaction between GAPC2 and ATG3. An RSV CP mutant that was unable to bind GAPC2 failed to disrupt the interaction between GAPC2 and ATG3 and therefore lost its ability to induce autophagy. RSV CP enhanced the autophagic degradation of a viral movement protein (MP) encoded by a heterologous virus, citrus leaf blotch virus (CLBV). However, the autophagic degradation of RSV-encoded MP and RNA-silencing suppressor (NS3) proteins was inhibited in the presence of CP, suggesting that RSV CP can protect MP and NS3 against autophagic degradation. Moreover, in the presence of MP, RSV CP could induce the autophagic degradation of a remorin protein (NbREM1), which negatively regulates RSV infection through the inhibition of viral cell-to-cell movement. Overall, our results suggest that RSV CP induces a selective autophagy to suppress the antiviral factors while protecting RSV-encoded viral proteins against autophagic degradation through an as-yet-unknown mechanism. This study showed that RSV CP plays dual roles in the autophagy-related interaction between plants and viruses.
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Affiliation(s)
- Wanying Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Li Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Lipeng Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Tong Zhou
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210095, China
| | - Fei Yan
- Institute of Plant Virology, Ningbo University, Ningbo, 312362, China
| | - Heng Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Ying Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Ida Bagus Andika
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Liying Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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14
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Kwarteng DO, Gangoda M, Kooijman EE. The effect of methylated phosphatidylethanolamine derivatives on the ionization properties of signaling phosphatidic acid. Biophys Chem 2023; 296:107005. [PMID: 36934676 DOI: 10.1016/j.bpc.2023.107005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/07/2023] [Indexed: 03/16/2023]
Abstract
Phosphatidylethanolamine (PE) and Phosphatidylcholine (PC) are the most abundant glycerophospholipids in eukaryotic membranes. The differences in the physicochemical properties of their headgroups have contrasting modulatory effects on their interaction with intracellular macromolecules. As such, their overall impact on membrane structure and function differs significantly. Enzymatic methylation of PE's amine headgroup produces two methylated derivatives namely monomethyl PE (MMPE) and dimethyl PE (DMPE) which have physicochemical properties that generally range between that of PE and PC. Additionally, their influence on membrane properties differs from both PE and PC. Although variations in headgroup methylation have been reported to affect signaling pathways, the direct influence that these differences exert on the ionization properties of signaling phospholipids have not been investigated. Here, we briefly review membrane function and structure that are mediated by the differences in headgroup methylation between PE, MMPE, DMPE and PC. In addition, using 31P MAS NMR, we investigate the effect of these four phospholipids on the ionization properties of the ubiquitous signaling anionic lipid phosphatidic acid (PA). Our results show that PA's ionization properties are differentially affected by changes in phospholipid headgroup methylation. This could have important implications for PA-protein binding and hence physiological functions in cells where signaling events lead to changes in abundance of methylated PE derivatives in the membrane.
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Affiliation(s)
- Desmond Owusu Kwarteng
- Department of Biological Sciences, Kent State University, P.O. Box 5190, Kent, OH 44242, USA.
| | - Mahinda Gangoda
- Department of Chemistry & Biochemistry, Kent State University, P.O. Box 5190, Kent, OH 44242, USA
| | - Edgar E Kooijman
- Department of Biological Sciences, Kent State University, P.O. Box 5190, Kent, OH 44242, USA.
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15
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Schlossarek D, Zhang Y, Sokolowska EM, Fernie AR, Luzarowski M, Skirycz A. Don't let go: co-fractionation mass spectrometry for untargeted mapping of protein-metabolite interactomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:904-914. [PMID: 36575913 DOI: 10.1111/tpj.16084] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 12/20/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
The chemical complexity of metabolomes goes hand in hand with their functional diversity. Small molecules have many essential roles, many of which are executed by binding and modulating the function of a protein partner. The complex and dynamic protein-metabolite interaction (PMI) network underlies most if not all biological processes, but remains under-characterized. Herein, we highlight how co-fractionation mass spectrometry (CF-MS), a well-established approach to map protein assemblies, can be used for proteome and metabolome identification of the PMIs. We will review recent CF-MS studies, discuss the main advantages and limitations, summarize the available CF-MS guidelines, and outline future challenges and opportunities.
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Affiliation(s)
- Dennis Schlossarek
- Depeartment One, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Youjun Zhang
- Depeartment One, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Ewelina M Sokolowska
- Depeartment One, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Alisdair R Fernie
- Depeartment One, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Marcin Luzarowski
- Center for Molecular Biology Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Aleksandra Skirycz
- Depeartment One, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
- Boyce Thompson Institute, Ithaca, NY, 14850, USA
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14850, USA
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