Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Aspergillus Aff. Niger A2

TISSUE(S): Whole Body

SUBMITTER: Xianliang Ma

LAB HEAD: Yucheng Chi

PROVIDER: PXD028426 | Pride | 2022-07-31

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

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.

2021-06-01 | PXD026373 | Pride

Genome-wide Transcriptional Responses of the Filamentous Fungus Aspergillus niger to Lignocellulose (Wheat straw) using RNA-sequencing

Project description:We have studied the physiological response of the fungus Aspergillus niger when exposed to wheat straw as a model lignocellulosic substrate. Using RNA-sequencing we showed that, 24 hours after exposure to straw, gene expression of known plant cell wall degrading enzymes represents a huge investment for the cells (about 20 % of the total mRNA). Our results also uncovered new esterases and surface interacting proteins that might form part of the fungal degradative arsenal. We also show that antisense transcripts are abundant and that their expression can be regulated by conditions. Triplicate samples of A. niger N402 taken at each of three timepoints: After 48 h growth in minimal media with Glucose as sole carbon source, After transfer to Wheat Straw media for 24 h and 5 h after after the exogenous addition of glucose to the wheat starw media.

2012-08-27 | E-GEOD-33852 | biostudies-arrayexpress

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.

2024-01-26 | PXD041490 | Pride

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

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

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.

2021-06-10 | PXD020790 | Pride

Proteome-wide analyses reveal the diverse functions of lysine 2-hydroxyisobutyrylation in Oryza sativa

Project description:Lysine 2-hydroxyisobutyrylation (Khib), a newly identified post-translational modification, is known to regulate transcriptional activity in animals. However, extensive studies of the lysine 2-hydroxyisobutyrylome in plants and animals have yet to be performed. In this study, using LC-MS/MS qualitative proteomic strategies, we identified 4,163 Khib sites on 1,596 modified proteins in rice (Oryza sativa) seedlings. Motif analysis revealed 10 conserved motifs flanking the Khib sites, and subcellular localization analysis revealed that 44% of the Khib proteins are localized in the chloroplast. Gene ontology function, KEGG pathway, and protein domain enrichment analyses revealed that Khib occurs on proteins involved in diverse biological processes and is especially enriched in carbon metabolism and photosynthesis. Among the modified proteins, 20 Khib sites were identified in histone H2A and H2B, while only one site was identified in histone H4. Protein-protein interaction (PPI) network analysis further demonstrated that Khib participates in diverse biological processes including ribosomal activity, biosynthesis of secondary metabolites, and metabolic pathways. In addition, a comparison of lysine 2-hydroxyisobutyrylation, acetylation, and crotonylation in the rice proteome showed that 45 proteins with only 26 common lysine sites are commonly modified by three PTMs. The crosstalks of modified sites and PPI among these PTMs may form a complex network with both similar and different regulatory mechanisms. In summary, our study comprehensively profiles the lysine 2-hydroxyisobutyrylome in rice and provides a better understanding of its biological functions in plants.

2021-09-09 | PXD018778 | Pride

Proteome-wide analysis of Lysine 2-Hydroxyisobutyrylation in Candida albicans

Project description:Candida albicans is the most common human fungal pathogen, causing diseases ranging from mucosal to systemic infections for both immunocompetent and immunocompromised individuals. 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 C. albicans. 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 C. albicans. We identified 1438 Khib-modified proteins with 6659 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 antibiotics, biosynthesis of secondary metabolites, biosynthesis of amino acids and carbon metabolism – of which the ribosome pathway is the most affected pathway. Even when compared with the reported lysine acetylation (Kac) and succinylation (Ksuc), the Khib-modified sites on ribosomal proteins remained the highest for C. albicans. These bioinformatic results suggest that 2-hydroxyisobutyrylation may play an indispensable role in the regulation of the ribosomal biogenesis and protein translation. Confirmation at the biochemical level would enable us to resolve physiological and pathogenic roles of PTM in C. albicans.

2021-01-15 | PXD023013 | Pride

Global analysis of lysine 2-hydroxyisobutyrylation in wheat root

2021-09-09 | PXD020819 | Pride

Genomic and Proteomic characterization of Aspergillus niger isolated from the International Space Station

Project description:Genomic and proteomic characterization of the Aspergillus niger isolate, JSC-093350089, collected from U.S. segment surfaces of the International Space Station (ISS) is reported, along with a comparison to the experimentally established strain ATCC 1015. Whole-genome sequencing of JSC-093350089 revealed enhanced genetic variance when compared to publicly available sequences of A. niger strains. Analysis of the isolate’s proteome revealed significant differences in the molecular phenotype of JSC-093350089, including increased abundance of proteins involved in the A. niger starvation response, oxidative stress resistance, cell wall integrity and modulation, and nutrient acquisition. Together, these data reveal the existence of a distinct strain of A. niger onboard the ISS and provide insight into the molecular phenotype that is selected for by melanized fungal species inhabiting spacecraft environments.

2018-08-21 | PXD008588 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data