Global analysis of lysine acetylation reveals its role in multiple biological processes in Glycine max

2020 ◽  
Author(s):  
Geng Li ◽  
Bin Zheng ◽  
Wei Zhao ◽  
Ting-Hu Ren ◽  
Xing-Hui Zhang ◽  
...  
Keyword(s):  
Carbon Fixation ◽  
Global Analysis ◽  
Tca Cycle ◽  
Metabolic Process ◽  
Lysine Acetylation ◽  
Post Translational Modification ◽  
Ribose Phosphate ◽  
Core Histones ◽  
Proteomic Investigation ◽  
Soybean Leaves

Abstract Protein lysine acetylation (Kac) is an important post-translational modification present in both animal and plant cells. Here, we reported the results from a proteomic investigation of Kac in soybean leaves. We totally identified 3148 acetylation sites in 1538 proteins from three biological replicates, among 59 lysine acetylation sites in core histones, represents the largest acetylome dataset in plants to date. Gene Ontology (GO) functional analysis illustrated that most of the acetylated proteins involved in metabolic processes (include carboxylic acid metabolic process, oxoacid metabolic process, nucleoside metabolic process, nucleoside phosphate metabolic process, and ribose phosphate metabolic process). KEGG pathway enrichment showed Kac plays an important role in Photosynthesis, Carbon fixation in photosynthetic organisms and Citrate cycle (TCA cycle). Meanwhile we also find a total of 17 conserved Kac motifs. All together, our study not only provides the first global and most extensive lysine acetylation analysis in soybean leaves, but also suggest that lysine acetylation is play an important and unique role in plants.

scholarly journals Global analysis of lysine acetylation in soybean leaves

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Geng Li ◽  
Bin Zheng ◽  
Wei Zhao ◽  
Tinghu Ren ◽  
Xinghui Zhang ◽  
...  
Keyword(s):  
Protein Biosynthesis ◽  
Global Analysis ◽  
Subcellular Location ◽  
Structure Characterization ◽  
Lysine Acetylation ◽  
Post Translational Modification ◽  
Motif Analysis ◽  
Bioinformatics Analyses ◽  
Oil Crop ◽  
Soybean Leaves

AbstractProtein lysine acetylation (Kac) is an important post-translational modification in both animal and plant cells. Global Kac identification has been performed at the proteomic level in various species. However, the study of Kac in oil and resource plant species is relatively limited. Soybean is a globally important oil crop and resouce plant. In the present study, lysine acetylome analysis was performed in soybean leaves with proteomics techniques. Various bioinformatics analyses were performed to illustrate the structure and function of these Kac sites and proteins. Totally, 3148 acetylation sites in 1538 proteins were detected. Motif analysis of these Kac modified peptides extracted 17 conserved motifs. These Kac modified protein showed a wide subcellular location and functional distribution. Chloroplast is the primary subcellular location and cellular component where Kac proteins were localized. Function and pathways analyses indicated a plenty of biological processes and metabolism pathways potentially be influenced by Kac modification. Ribosome activity and protein biosynthesis, carbohydrate and energy metabolism, photosynthesis and fatty acid metabolism may be regulated by Kac modification in soybean leaves. Our study suggests Kac plays an important role in soybean physiology and biology, which is an available resource and reference of Kac function and structure characterization in oil crop and resource plant, as well as in plant kingdom.

scholarly journals Global analysis of lysine 2-hydroxyisobutyrylation in wheat root

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Feng Bo ◽  
Li Shengdong ◽  
Wang Zongshuai ◽  
Cao Fang ◽  
Wang Zheng ◽  
...  
Keyword(s):  
High Resolution Mass Spectrometry ◽  
Biological Activities ◽  
Global Analysis ◽  
Plant Root ◽  
Subcellular Location ◽  
Tca Cycle ◽  
Wheat Root ◽  
Post Translational Modification ◽  
Cellular Functions

AbstractLysine 2-hydroxyisobutyrylation (Khib) is a novel naturally occurring post-translational modification. The system Khib identification at proteomics level has been performed in various species and tissues to characterize the role of Khib in biological activities. However, the study of Khib in plant species is relatively less. In the present study, the first plant root tissues lysine 2-hydroxyisobutyrylome analysis was performed in wheat with antibody immunoprecipitation affinity, high resolution mass spectrometry-based proteomics and bioinformatics analysis. In total, 6328 Khib sites in 2186 proteins were repeatedly identified in three replicates. These Khib proteins showed a wide subcellular location distribution. Function and pathways characterization of these Khib proteins indicated that many cellular functions and metabolism pathways were potentially affected by this modification. Protein and amino acid metabolism related process may be regulated by Khib, especially ribosome activities and proteins biosynthesis process. Carbohydrate metabolism and energy production related processes including glycolysis/gluconeogenesis, TCA cycle and oxidative phosphorylation pathways were also affected by Khib modification. Besides, root sulfur assimilation and transformation related enzymes exhibited Khib modification. Our work illustrated the potential regulation role of Khib in wheat root physiology and biology, which could be used as a useful reference for Khib study in plant root.

scholarly journals Acetylation Profiles in the Metabolic Process of Glioma-Associated Seizures

2021 ◽  
Vol 12 ◽  
Author(s):  
Ya-Wen Xu ◽  
Peng Lin ◽  
Shu-Fa Zheng ◽  
Wen Huang ◽  
Zhang-Ya Lin ◽  
...  
Keyword(s):  
Oxidative Phosphorylation ◽  
Western Blot ◽  
Quantitative Proteomics ◽  
Tca Cycle ◽  
Metabolic Process ◽  
Lysine Acetylation ◽  
Protein Acetylation ◽  
Label Free ◽  
The Tca Cycle ◽  
Proteomic Study

Objective: We test the hypothesis that lysine acetylation is involved in the metabolic process of glioma-associated seizures (GAS).Methods: We used label-free mass spectrometry-based quantitative proteomics to quantify dynamic changes of protein acetylation between gliomas with seizure (CA1 group) and gliomas without seizure (CA2 group). Furthermore, differences of acetyltransferase and deacetylase expression between CA1 and CA2 groups were performed by a quantitative proteomic study. We further classified acetylated proteins into groups according to cell component, molecular function, and biological process. In addition, metabolic pathways and protein interaction networks were analyzed. Regulated acetyltransferases and acetylated profiles were validated by PRM and Western blot.Results: We detected 169 downregulated lysine acetylation sites of 134 proteins and 39 upregulated lysine acetylation sites of 35 proteins in glioma with seizures based on acetylome. We detected 407 regulated proteins by proteomics, from which ACAT2 and ACAA2 were the differentially regulated enzymes in the acetylation of GAS. According to the KEGG analysis, the upregulated acetylated proteins within the PPIs were mapped to pathways involved in the TCA cycle, oxidative phosphorylation, biosynthesis of amino acids, and carbon metabolism. The downregulated acetylated proteins within the PPIs were mapped to pathways involved in fatty acid metabolism, oxidative phosphorylation, TCA cycle, and necroptosis. Regulated ACAT2 expression and acetylated profiles were validated by PRM and Western blot.Conclusions: The data support the hypothesis that regulated protein acetylation is involved in the metabolic process of GAS, which may be induced by acetyl-CoA acetyltransferases.

scholarly journals First nitrosoproteomic profiling deciphers the cysteine S-nitrosylation involved in multiple metabolic pathways of tea leaves

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Chen Qiu ◽  
Jianhao Sun ◽  
Yu Wang ◽  
Litao Sun ◽  
Hui Xie ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Global Analysis ◽  
Alcoholic Beverage ◽  
Calvin Cycle ◽  
Tca Cycle ◽  
Functional Enrichment ◽  
Post Translational Modification ◽  
Tea Leaves ◽  
Solid Foundation ◽  
Tea Plants

AbstractCysteine S-nitrosylation is a reversible protein post-translational modification and critically regulates the activity, localization and stability of proteins. Tea (Camellia sinensis (L.) O. Kuntze) is one of the most thoroughly studied evergreen crop due to its broad non-alcoholic beverage and huge economic impact in the world. However, little is known about the S-nitrosylome in this plant. Here, we performed a global analysis of cysteine S-nitrosylation in tea leaves. In total, 228 cysteine S-nitrosylation sites were identified in 191 proteins, representing the first extensive data on the S-nitrosylome in tea plants. These S-nitrosylated proteins were located in various subcellular compartments, especially in the chloroplast and cytoplasm. Furthermore, the analysis of functional enrichment and PPI network revealed that the S-nitrosylated proteins were mainly involved in multiple metabolic pathways, including glycolysis, pyruvate metabolism, Calvin cycle and TCA cycle. Overall, this study not only systematically identified the proteins of S-nitrosylation in cysteines of tea leaves, but also laid the solid foundation for further verifying the roles of S-nitrosylation in cysteines of tea plants.

scholarly journals First comprehensive analysis of lysine succinylation in paper mulberry (Broussonetia papyrifera)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yibo Dong ◽  
Ping Li ◽  
Ping Li ◽  
Chao Chen
Keyword(s):  
Oxidative Phosphorylation ◽  
Carbon Fixation ◽  
Economic Value ◽  
Glyoxylic Acid ◽  
Tca Cycle ◽  
Limited Information ◽  
Post Translational Modification ◽  
Cellular Processes ◽  
Lysine Succinylation ◽  
And Function

Abstract Background Lysine succinylation is a naturally occurring post-translational modification (PTM) that is ubiquitous in organisms. Lysine succinylation plays important roles in regulating protein structure and function as well as cellular metabolism. Global lysine succinylation at the proteomic level has been identified in a variety of species; however, limited information on lysine succinylation in plant species, especially paper mulberry, is available. Paper mulberry is not only an important plant in traditional Chinese medicine, but it is also a tree species with significant economic value. Paper mulberry is found in the temperate and tropical zones of China. The present study analyzed the effects of lysine succinylation on the growth, development, and physiology of paper mulberry. Results A total of 2097 lysine succinylation sites were identified in 935 proteins associated with the citric acid cycle (TCA cycle), glyoxylic acid and dicarboxylic acid metabolism, ribosomes and oxidative phosphorylation; these pathways play a role in carbon fixation in photosynthetic organisms and may be regulated by lysine succinylation. The modified proteins were distributed in multiple subcellular compartments and were involved in a wide variety of biological processes, such as photosynthesis and the Calvin-Benson cycle. Conclusion Lysine-succinylated proteins may play key regulatory roles in metabolism, primarily in photosynthesis and oxidative phosphorylation, as well as in many other cellular processes. In addition to the large number of succinylated proteins associated with photosynthesis and oxidative phosphorylation, some proteins associated with the TCA cycle are succinylated. Our study can serve as a reference for further proteomics studies of the downstream effects of succinylation on the physiology and biochemistry of paper mulberry.

scholarly journals Transcriptomic Analysis of the Photosynthetic, Respiration, and Aerenchyma Adaptation Strategies in Bermudagrass (Cynodon dactylon) under Different Submergence Stress

2021 ◽  
Vol 22 (15) ◽  
pp. 7905
Author(s):  
Zhongxun Yuan ◽  
Xilu Ni ◽  
Muhammad Arif ◽  
Zhi Dong ◽  
Limiao Zhang ◽  
...  
Keyword(s):  
Carbon Fixation ◽  
Cynodon Dactylon ◽  
Chlorophyll Biosynthesis ◽  
Tca Cycle ◽  
Ethylene Signaling ◽  
Physiological Mechanisms ◽  
Cell Wall Modification ◽  
Aerenchyma Formation ◽  
Submergence Stress ◽  
Photosynthesis And Respiration

Submergence impedes photosynthesis and respiration but facilitates aerenchyma formation in bermudagrass. Still, the regulatory genes underlying these physiological responses are unclear in the literature. To identify differentially expressed genes (DEGs) related to these physiological mechanisms, we studied the expression of DEGs in aboveground and underground tissues of bermudagrass after a 7 d treatment under control (CK), shallow submergence (SS), and deep submergence (DS). Results show that compared with CK, 12276 and 12559 DEGs were identified under SS and DS, respectively. Among them, the DEGs closely related to the metabolism of chlorophyll biosynthesis, light-harvesting, protein complex, and carbon fixation were down-regulated in SS and DS. Meanwhile, a large number of DEGs involved in starch and sucrose hydrolase activities, glycolysis/gluconeogenesis, tricarboxylic acid (TCA) cycle, and oxidative phosphorylation were down-regulated in aboveground tissues of bermudagrass in SS and DS. Whereas in underground tissues of bermudagrass these DEGs were all up-regulated under SS, only beta-fructofuranosidase and α-amylase related genes were up-regulated under DS. In addition, we found that DEGs associated with ethylene signaling, Ca2+-ROS signaling, and cell wall modification were also up-regulated during aerenchyma formation in underground tissues of bermudagrass under SS and DS. These results provide the basis for further exploration of the regulatory and functional genes related to the adaptability of bermudagrass to submergence.

scholarly journals Comment on ‘YcgC represents a new protein deacetylase family in prokaryotes’

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Magdalena Kremer ◽  
Nora Kuhlmann ◽  
Marius Lechner ◽  
Linda Baldus ◽  
Michael Lammers
Keyword(s):  
Lysine Acetylation ◽  
Post Translational Modification ◽  
Donor Molecule ◽  
Acetyl Coa ◽  
Lysine Deacetylases ◽  
Protein Deacetylase ◽  
New Protein

Lysine acetylation is a post-translational modification that is conserved from bacteria to humans. It is catalysed by the activities of lysine acetyltransferases, which use acetyl-CoA as the acetyl-donor molecule, and lysine deacetylases, which remove the acetyl moiety. Recently, it was reported that YcgC represents a new prokaryotic deacetylase family with no apparent homologies to existing deacetylases (Tu et al., 2015). Here we report the results of experiments which demonstrate that YcgC is not a deacetylase.

scholarly journals Transcriptome sequencing of Saccharina japonica sporophytes during whole developmental periods reveals regulatory networks underlying alginate and mannitol biosynthesis

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Zhanru Shao ◽  
Pengyan Zhang ◽  
Chang Lu ◽  
Shaoxuan Li ◽  
Zhihang Chen ◽  
...  
Keyword(s):  
Transcriptome Sequencing ◽  
Ribosomal Proteins ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Carbon Fixation ◽  
Brown Seaweed ◽  
Saccharina Japonica ◽  
Tca Cycle ◽  
New Genes ◽  
Mannitol Metabolism

Abstract Background Alginate is an important cell wall component and mannitol is a soluble storage carbon substance in the brown seaweed Saccharina japonica. Their contents vary with kelp developmental periods and harvesting time. Alginate and mannitol regulatory networks and molecular mechanisms are largely unknown. Results With WGCNA and trend analysis of 20,940 known genes and 4264 new genes produced from transcriptome sequencing of 30 kelp samples from different stages and tissues, we deduced that ribosomal proteins, light harvesting complex proteins and “imm upregulated 3” gene family are closely associated with the meristematic growth and kelp maturity. Moreover, 134 and 6 genes directly involved in the alginate and mannitol metabolism were identified, respectively. Mannose-6-phosphate isomerase (MPI2), phosphomannomutase (PMM1), GDP-mannose 6-dehydrogenase (GMD3) and mannuronate C5-epimerase (MC5E70 and MC5E122) are closely related with the high content of alginate in the distal blade. Mannitol accumulation in the basal blade might be ascribed to high expression of mannitol-1-phosphate dehydrogenase (M1PDH1) and mannitol-1-phosphatase (M1Pase) (in biosynthesis direction) and low expression of mannitol-2-dehydrogenase (M2DH) and Fructokinase (FK) (in degradation direction). Oxidative phosphorylation and photosynthesis provide ATP and NADH for mannitol metabolism whereas glycosylated cycle and tricarboxylic acid (TCA) cycle produce GTP for alginate biosynthesis. RNA/protein synthesis and transportation might affect alginate complex polymerization and secretion processes. Cryptochrome (CRY-DASH), xanthophyll cycle, photosynthesis and carbon fixation influence the production of intermediate metabolite of fructose-6-phosphate, contributing to high content of mannitol in the basal blade. Conclusions The network of co-responsive DNA synthesis, repair and proteolysis are presumed to be involved in alginate polymerization and secretion, while upstream light-responsive reactions are important for mannitol accumulation in meristem of kelp. Our transcriptome analysis provides new insights into the transcriptional regulatory networks underlying the biosynthesis of alginate and mannitol during S. japonica developments.

scholarly journals Comprehensive Proteome and Lysine Acetylome Analysis Reveals the Widespread Involvement of Acetylation in Cold Resistance of Pepper (Capsicum annuum L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhoubin Liu ◽  
Jingshuang Song ◽  
Wu Miao ◽  
Bozhi Yang ◽  
Zhuqing Zhang ◽  
...  
Keyword(s):  
Cold Stress ◽  
Carbon Fixation ◽  
Cold Resistance ◽  
Triosephosphate Isomerase ◽  
Carbon Assimilation ◽  
Differentially Expressed ◽  
Lysine Acetylation ◽  
Bisphosphate Carboxylase ◽  
Pepper Leaves ◽  
Assimilation Capacity

Pepper is a typical warmth-loving vegetable that lacks a cold acclimation mechanism and is sensitive to cold stress. Lysine acetylation plays an important role in diverse cellular processes, but limited knowledge is available regarding acetylation modifications in the resistance of pepper plants to cold stress. In this study, the proteome and acetylome of two pepper varieties with different levels of cold resistance were investigated by subjecting them to cold treatments of varying durations followed by recovery periods. In total, 6,213 proteins and 4,574 lysine acetylation sites were identified, and this resulted in the discovery of 3,008 differentially expressed proteins and 768 differentially expressed acetylated proteins. A total of 1,988 proteins were identified in both the proteome and acetylome, and the functional differences in these co-identified proteins were elucidated through GO enrichment. KEGG analysis showed that 397 identified acetylated proteins were involved in 93 different metabolic pathways. The dynamic changes in the acetylated proteins in photosynthesis and the “carbon fixation in the photosynthetic organisms” pathway in pepper under low-temperature stress were further analyzed. It was found that acetylation of the PsbO and PsbR proteins in photosystem II and the PsaN protein in photosystem I could regulate the response of pepper leaves to cold stress. The acetylation levels of key carbon assimilation enzymes, such as ribulose bisphosphate carboxylase, fructose-1,6-bisphosphatase, sedoheptulose-1,7-bisphosphatase, glyceraldehyde 3-phosphate dehydrogenase, phosphoribulokinase, and triosephosphate isomerase decreased, leading to decreases in carbon assimilation capacity and photosynthetic efficiency, reducing the cold tolerance of pepper leaves. This study is the first to identify the acetylome in pepper, and it greatly expands the catalog of lysine acetylation substrates and sites in Solanaceae crops, providing new insights for posttranslational modification studies.

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