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.

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 Systematic analysis of lysine 2-hydroxyisobutyrylation posttranslational modification in wheat leaves

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0253325
Author(s):  
Bo Feng ◽  
Shengdong Li ◽  
Zongshuai Wang ◽  
Fang Cao ◽  
Zheng Wang ◽  
...  
Keyword(s):  
Plant Species ◽  
Protein Biosynthesis ◽  
Critical Role ◽  
Subcellular Location ◽  
Structure Characterization ◽  
Sequence Motifs ◽  
Post Translational Modification ◽  
Subcellular Compartment ◽  
Conserved Sequence ◽  
Cereal Plant

Lysine 2-hydroxyisobutyrylation (Khib) is a recently discovered post-translational modification (PTM) showing diverse biological functions and effects in living organisms. However, the study of Khib in plant species is still relatively limited. Wheat (Triticum aestivum L.) is a global important cereal plant. In this study, the systematic Khib analysis was performed in wheat leave tissues. A total of 3004 Khib sites in 1104 proteins were repeatedly identified. Structure characterization of these Khib peptides revealed 12 conserved sequence motifs. Function classification and enrichment analysis indicated these Khib proteins showed a wide function and pathway distribution, of which ribosome activity, protein biosynthesis and photosynthesis were the preferred biological processes. Subcellular location predication indicated chloroplast was the dominant subcellular compartment where Khib was distributed. There may be some crosstalks among Khib, lysine acetylation and lysine succinylation modification because some proteins and sites were modified by all these three acylations. The present study demonstrated the critical role of Khib in wheat biological and physiology, which has expanded the scope of Khib in plant species. Our study is an available resource and reference of Khib function demonstration and structure characterization in cereal 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 Comparative phosphoproteome analysis to identify candidate phosphoproteins involved in blue light-induced brown film formation in Lentinula edodes

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9859
Author(s):  
Tingting Song ◽  
Yingyue Shen ◽  
Qunli Jin ◽  
Weilin Feng ◽  
Lijun Fan ◽  
...  
Keyword(s):  
Blue Light ◽  
Molecular Mechanisms ◽  
Lentinula Edodes ◽  
Film Formation ◽  
Quantitative Information ◽  
Light Signal ◽  
Post Translational Modification ◽  
Bioinformatics Analyses ◽  
Phosphorylated Proteins ◽  
Liquid Chromatography Tandem Mass

Light plays an important role in the growth and differentiation of Lentinula edodes mycelia, and mycelial morphology is influenced by light wavelengths. The blue light-induced formation of brown film on the vegetative mycelial tissues of L. edodes is an important process. However, the mechanisms of L. edodes’ brown film formation, as induced by blue light, are still unclear. Using a high-resolution liquid chromatography-tandem mass spectrometry integrated with a highly sensitive immune-affinity antibody method, phosphoproteomes of L. edodes mycelia under red- and blue-light conditions were analyzed. A total of 11,224 phosphorylation sites were identified on 2,786 proteins, of which 9,243 sites on 2,579 proteins contained quantitative information. In total, 475 sites were up-regulated and 349 sites were down-regulated in the blue vs red group. To characterize the differentially phosphorylated proteins, systematic bioinformatics analyses, including gene ontology annotations, domain annotations, subcellular localizations, and Kyoto Encyclopedia of Genes and Genomes pathway annotations, were performed. These differentially phosphorylated proteins were correlated with light signal transduction, cell wall degradation, and melanogenesis, suggesting that these processes are involved in the formation of the brown film. Our study provides new insights into the molecular mechanisms of the blue light-induced brown film formation at the post-translational modification level.

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.

Comparative phosphoproteome analysis to identify candidate phosphoproteins involved in blue light-induced brown film formation in Lentinula edodes

2020 ◽  
Author(s):  
Tingting Song ◽  
Yingyue Shen ◽  
Qunli Jin ◽  
Weilin Feng ◽  
Lijun Fan ◽  
...  
Keyword(s):  
Blue Light ◽  
Molecular Mechanisms ◽  
Lentinula Edodes ◽  
Film Formation ◽  
Quantitative Information ◽  
Light Signal ◽  
Post Translational Modification ◽  
Bioinformatics Analyses ◽  
Phosphorylated Proteins ◽  
Liquid Chromatography Tandem Mass

Abstract BackgroundLight plays an important role in the growth and differentiation of Lentinula edodes mycelia, and mycelial morphology is influenced by light wavelengths. The blue light-induced formation of brown film on the vegetative mycelial tissues of L. edodes is an important process. However, the mechanisms of L. edodes’ brown film formation, as induced by blue light, are still unclear. Using a high-resolution liquid chromatography-tandem mass spectrometry integrated with a highly sensitive immune-affinity antibody method, phosphoproteomes of L. edodes mycelia under red- and blue-light conditions were analyzed. ResultsA total of 11,224 phosphorylation sites were identified on 2,786 proteins, of which 9,243 sites on 2,579 proteins contained quantitative information. In total, 475 sites were up-regulated and 349 sites were down-regulated in the blue vs red group. To characterize the differentially phosphorylated proteins, systematic bioinformatics analyses, including gene ontology annotations, domain annotations, subcellular localizations, and Kyoto Encyclopedia of Genes and Genomes pathway annotations, were performed. These differentially phosphorylated proteins were correlated with light signal transduction, cell wall degradation, and melanogenesis, suggesting that these processes are involved in the formation of the brown film. ConclusionsOur study provides new insights into the molecular mechanisms of the blue light-induced brown film formation at the post-translational modification level.

scholarly journals Profiling of lysine-acetylated proteins in human urine

2017 ◽  
Author(s):  
Weiwei Qin ◽  
Zhenhuan Du ◽  
He Huang ◽  
Youhe Gao
Keyword(s):  
Human Urine ◽  
High Resolution Mass Spectrometry ◽  
The Body ◽  
Lysine Acetylation ◽  
Biological Processes ◽  
Post Translational Modification ◽  
Post Translational Modifications ◽  
Normal Human ◽  
Measurable Change

AbstractBiomarker is the measurable change associated with a physiological or pathophysiological process, its nature is change. Contrast to the blood which is under homeostatic controls, urine reflects changes in the body earlier and more sensitive therefore is a better biomarker source. Lysine acetylation is an abundant and highly regulated post-translational modification. It plays a pivotal role in modulating diverse biological processes and is associated with various important diseases. Enrichment or visualization of proteins with specific post-translational modifications provides a method for sampling the urinary proteome and reducing sample complexity. In this study, we used anti-acetyllysine antibody-based immunoaffinity enrichment combined with high-resolution mass spectrometry to profile lysine-acetylated proteins in normal human urine. A total of 629 acetylation sites on 315 proteins were identified, including some very low-abundance proteins. This is the first proteome-wide characterization of lysine acetylation proteins in normal human urine. Our dataset provides a useful resource for the further discovery of the lysine acetylated proteins as biomarker in urine.

scholarly journals Global Lysine Acetylome Analysis of LPS-Stimulated HepG2 Cells Identified Hyperacetylation of PKM2 as a Metabolic Regulator in Sepsis

2021 ◽  
Vol 22 (16) ◽  
pp. 8529
Author(s):  
Ann-Yae Na ◽  
Sanjita Paudel ◽  
Soyoung Choi ◽  
Jun Hyung Lee ◽  
Min-Sik Kim ◽  
...  
Keyword(s):  
Liver Dysfunction ◽  
Lactate Level ◽  
Hepg2 Cells ◽  
Lactate Concentration ◽  
Lysine Acetylation ◽  
Post Translational Modification ◽  
Glycolysis Pathway ◽  
The Relationship ◽  
Causative Link ◽  
Lps Treatment

Sepsis-induced liver dysfunction (SILD) is a common event and is strongly associated with mortality. Establishing a causative link between protein post-translational modification and diseases is challenging. We studied the relationship among lysine acetylation (Kac), sirtuin (SIRTs), and the factors involved in SILD, which was induced in LPS-stimulated HepG2 cells. Protein hyperacetylation was observed according to SIRTs reduction after LPS treatment for 24 h. We identified 1449 Kac sites based on comparative acetylome analysis and quantified 1086 Kac sites on 410 proteins for acetylation. Interestingly, the upregulated Kac proteins are enriched in glycolysis/gluconeogenesis pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) category. Among the proteins in the glycolysis pathway, hyperacetylation, a key regulator of lactate level in sepsis, was observed at three pyruvate kinase M2 (PKM2) sites. Hyperacetylation of PKM2 induced an increase in its activity, consequently increasing the lactate concentration. In conclusion, this study is the first to conduct global profiling of Kac, suggesting that the Kac mechanism of PKM2 in glycolysis is associated with sepsis. Moreover, it helps to further understand the systematic information regarding hyperacetylation during the sepsis process.

scholarly journals Global analysis of lysine succinylation in patchouli plant leaves

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Xiaobing Wang ◽  
Xiuzhen Chen ◽  
Junren Li ◽  
Xuanxuan Zhou ◽  
Yanting Liu ◽  
...  
Keyword(s):  
Global Analysis ◽  
Functional Characterization ◽  
Subcellular Location ◽  
Tca Cycle ◽  
Industrial Plant ◽  
Enrichment Technique ◽  
Affinity Enrichment ◽  
Lysine Succinylation ◽  
Living Organisms

AbstractLysine succinylation is a novel, naturally occurring posttranslational modification (PTM) in living organisms. Global lysine succinylation identification has been performed at the proteomic level in various species; however, the study of lysine succinylation in plant species is relatively limited. Patchouli plant (P. cablin (Blanco) Benth., Lamiaceae) is a globally important industrial plant and medicinal herb. In the present study, lysine succinylome analysis was carried out in patchouli plants to determine the potential regulatory role of lysine succinylation in patchouli growth, development, and physiology. The global succinylation sites and proteins in patchouli plants were screened with an immunoprecipitation affinity enrichment technique and advanced mass spectrometry-based proteomics. Several bioinformatic analyses, such as function classification and enrichment, subcellular location predication, metabolic pathway enrichment and protein−protein interaction networking, were conducted to characterize the functions of the identified sites and proteins. In total, 1097 succinylation sites in 493 proteins were detected in patchouli plants, among which 466 succinylation sites in 241 proteins were repeatedly identified within three independent experiments. The functional characterization of these proteins indicated that the tricarboxylic acid (TCA) cycle, oxidative phosphorylation, photosynthesis processes, and amino acid biosynthesis may be regulated by lysine succinylation. In addition, these succinylated proteins showed a wide subcellular location distribution, although the chloroplast and cytoplasm were the top two preferred cellular components. Our study suggested the important role of lysine succinylation in patchouli plant physiology and biology and could serve as a useful reference for succinylation studies in other medicinal plants.

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