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Global analysis of lysine 2-hydroxyisobutyrylation in wheat root

ABSTRACT: Lysine 2-hydroxyisobutyrylation (Khib) is a novel naturally occurring PTM, which is firstly discovered in histone. The system Khib detection at proteomics level has been performed in various species and tissues for the function and role characterization of Khib in biological activities. However, the Khib study in plant species is relatively less and the plant root, one of the critical plant organ, haven’t been studied. In the present study, the first root tissues lysine 2-hydroxyisobutyrylome analysis was performed in wheat specie with antibody immunoprecipitation affinity and high resolution mass spectrometry-based proteomics. Bioinformatics analyses including function classification, subcellular location predication, gene ontology enrichment and pathway enrichment were conducted to demonstrate the roles of these Khib sites and proteins in wheat root.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Triticum Aestivum (wheat)

TISSUE(S): Root

SUBMITTER: Xianliang Ma

LAB HEAD: Geng Li

PROVIDER: PXD020819 | Pride | 2021-09-09

REPOSITORIES: pride

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			Action	DRS
	Wheatroot.rar	Other
	XMG-IP-1.raw	Raw
	XMG-IP-2.raw	Raw
	XMG-IP-3.raw	Raw

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Publications

Global analysis of lysine 2-hydroxyisobutyrylation in wheat root.

Bo Feng F Shengdong Li L Zongshuai Wang W Fang Cao C Zheng Wang W Chunhua Gao G Geng Li L Ling'an Kong K

Scientific reports 20210318 1

Lysine 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 ...[more]

PMID: 33737719

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Global analysis of lysine 2-hydroxyisobutyrylation in wheat leaf

2021-06-10 | PXD020790 | Pride

Global analysis of lysine 2-hydroxyisobutyrylation in wheat leaf

Project description:Lysine 2-hydroxyisobutyrylation (Khib) is a novel naturally occurring PTM, which is firstly discovered in histone. The system Khib detection at proteomics level has been performed in various species and tissues for the function and role characterization of Khib in biological activities. However, the Khib study in plant species is relatively less and the plant root, one of the critical plant organ, haven’t been studied. In the present study, the first root tissues lysine 2-hydroxyisobutyrylome analysis was performed in wheat specie with antibody immunoprecipitation affinity and high resolution mass spectrometry-based proteomics. Bioinformatics analyses including function classification, subcellular location predication, gene ontology enrichment and pathway enrichment were conducted to demonstrate the roles of these Khib sites and proteins in wheat root. In total, 6328 Khib sites corresponding to 2186 proteins were repeatedly identified in three replicates. These Khib proteins showed a wide subcellular location distribution while cytoplasm was the primary subcellular compartment where Khib protein located. Function and pathways characterization of these Khib proteins indicated that many cellular functions and metabolism pathways potentially were 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 the hotspots where protein Khib occurred. Our work illustrated the potential regulation role of Khib in wheat leaf physiology and biology, which could be used as a useful reference for Khib studies in plant leaf.

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Global analysis of lysine 2-hydroxyisobutyrylation in Rheum palmatum

Project description:Lysine 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.

2021-03-29 | PXD024730 | Pride

Global analysis of lysine 2-hydroxyisobutyrylation in Glycine max

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Lysine 2-hydroxyisobutyrylatome profiling reveals extensive lysine 2-hydroxyisobutyrylation in common wheat

Project description:In this work, we first analyzed wheat (Triticum aestivum L.) lysine Khib sites by mass spectrometry. A total of 3,348 lysine modification sites from 1,047 proteins were identified in wheat seedlings. The identified Kcr proteins were discovered to be widespread. Bioinformatic data indicated these Kcr proteins involved in diverse biology and metabolic processes. Our data indicated that Khib is as dynamic as Kac and Khib changes in response to the deacetylase inhibitors Trichostatin A (TSA) and nicotinamide (NAM). We tested histone Khib and deacylation activities of several wheat HATs and HDACs using wheat Krnose EMS mutants. Finally, we confirmed lysine Khib on K206 of PGK was a regulatory modification using mustagenesis experiments and found that de-Khib impaired protein interactions of PGK. Our data demonstrate that the regulatory scope of lysine Khib is broad and comparable with that of other major PTMs. Wheat histone Khib are dynamically regulated by environmental cues and are likely to be removed by different mechanisms.

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Systematic analysis of lysine 2-hydroxyisobutyrylation in Rheum palmatum L． leaves

Project description:Lysine 2-hydroxyisobutyrylation (Khib) is a recently discovered posttranslational modification (PTM). Its structure characterization and function illustration have been reported in some species. However, the study of Khib in plant species is still relatively limited.Rheum palmatum L. is a global important plant. In this study, the first wheat global Khib analysis was performed with leave tissues; with the purpose of uncover the possible biological and physiological role of Khib in Rheum palmatum L.growth and development. Antibody based affinity enrichment technique was used to capture the modified peptides and high resolution mass spectrometry combining bioinformatics was applied to detect and decipher the Khib sites and proteins.

2021-05-29 | PXD026307 | Pride

Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylation in the Aspergillus niger in Peanuts

Project description:Aspergillus niger is a very destructive pathogen causing severe peanut root rot, especially in the seeding stage of peanuts (Arachis hypogaea), and often leading to the death of the plant. Protein lysine 2-hydroxyisobutyrylation (Khib) is a newly detected post-translational modification identified in several species. In this study, we identified 5041 Khib sites on 1453 modified proteins in A. niger. Compared with five other species, A. niger has conserved and novel proteins. Bioinformatics analysis showed that Khib proteins are widely distributed in A. niger and are involved in many biological processes. GO and KEGG enrichment analyses revealed that Khib proteins were significantly enriched in many cellular compartments and pathways, such as ribosomes and proteasome subunits. A total of 223 Knib proteins were part of the PPI network, thus, suggesting that Knib proteins are associated with a large range of protein interactions and diverse pathways in the life processes of A. niger. Several identified proteins are involved in pathogenesis regulation. Our research provides the first comprehensive report of lysine 2-hydroxyisobutyrylation and an extensive database for potential functional studies on Knib proteins in this economically important fungus.

2022-07-31 | PXD028426 | Pride

Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylation in the Aspergillus niger in Peanuts

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RNA-seq Transcriptional Profiling of Herbaspirillum seropedicae Colonizing Bread Wheat (Triticum aestivum) Roots.

Project description:H. seropedicae is a diazotrophic and endophytic bacterium that associates with economically important grasses promoting plant growth and increasing productivity. To identify genes related to bacterial ability to colonize and promote plant growth wheat seedlings growing hydroponically in Hoaglandâs medium were inoculated with H. seropedicae the bacteria and incubated for 3 days. mRNA from the bacteria present in the root surface and in the plant medium were purified, depleted from rRNA and used for RNA-seq profiling. RT-qPCR analyses were conducted to confirm regulation of selected genes. Comparison of RNA profile of bacteria attached to the root and planktonic revealed an extensive metabolic adaptation to the epiphytic life style.

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Proteome-wide analysis of Lysine 2-Hydroxyisobutyrylation in Aspergillus fumigatus

Project description:Aspergillus fumigatus is the main culprit of invasive aspergillosis, which has a high mortality rate in immunocompromised patients. Lysine 2-hydroxyisobutyrylation is a highly conserved posttranslational modification found in a wide variety of organisms. In this study, we survey the biological impact of 2-hydroxyisobutyrylation on lysine residuals (Khib) in A. fumigatus. Using an antibody-enrichment approach along with the traditional LC-MS/MS method, the pattern of Khib-modified proteins and sites were analyzed in one wild type strain of A. fumigatus. We identified 3494 Khib-modified proteins with 18091 modified sites in this strain, and a more detailed bioinformatics analysis indicated that the Khib-modified proteins are involved in a wide range of cellular functions with diverse subcellular locations. Functional enrichment analysis featured several prominent functional pathways, including ribosome, biosynthesis of amino acids and nucleocytoplasmic transport – of which the ribosome pathway is the most affected pathway. When compared with other reported Khib eukaryotes, both Khib-modified sites and Khib-modified proteins also remained the highest. It proves that this modification is of great importance in A. fumigatus. At the same time, several enzymes in the fungal ergosterol synthesis pathway are modified with Khib. These bioinformatic results suggest that 2-hydroxyisobutyrylation may play an indispensable role in the regulation of the ribosomal biogenesis and the process of fungal resistance. Findings in this study may provide new insights for studying PTM-associated mechanisms in fungal development and antifungal drug development.

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