Dataset Information

Global analysis of protein lysine 2-hydroxyisobutyrylation (K_hib) profiles in Chinese herb rhubarb (Dahuang).

ABSTRACT:

Background

Lysine 2-hydroxyisobutyrylation (K_hib) is a newly discovered protein posttranslational modification (PTM) and is involved in the broad-spectrum regulation of cellular processes that are found in both prokaryotic and eukaryotic cells, including in plants. The Chinese herb rhubarb (Dahuang) is one of the most widely used traditional Chinese medicines in clinical applications. To better understand the physiological activities and mechanism of treating diseases with the herb, it is necessary to conduct intensive research on rhubarb. However, K_hib modification has not been reported thus far in rhubarb.

Results

In this study, we performed the first global analysis of K_hib-modified proteins in rhubarb by using sensitive affinity enrichment combined with high-accuracy HPLC-MS/MS tandem spectrometry. A total of 4333 overlapping K_hib modification peptides matched on 1525 K_hib-containing proteins were identified in three independent tests. Bioinformatics analysis showed that these K_hib-containing proteins are involved in a wide range of cellular processes, particularly in protein biosynthesis and central carbon metabolism and are distributed mainly in chloroplasts, cytoplasm, nucleus and mitochondria. In addition, the amino acid sequence motif analysis showed that a negatively charged side chain residue (E), a positively charged residue (K), and an uncharged residue with the smallest side chain (G) were strongly preferred around the K_hib site, and a total of 13 K_hib modification motifs were identified. These identified motifs can be classified into three motif patterns, and some motif patterns are unique to rhubarb and have not been identified in other plants to date.

Conclusions

A total of 4333 K_hib-modified peptides on 1525 proteins were identified. The K_hib-modified proteins are mainly distributed in the chloroplast, cytoplasm, nucleus and mitochondria, and involved in a wide range of cellular processes. Moreover, three types of amino acid sequence motif patterns, including EK_hib/K_hibE, GK_hib and k.kkk….K_hib….kkkkk, were extracted from a total of 13 K_hib-modified peptides. This study provides comprehensive K_hib-proteome resource of rhubarb. The findings from the study contribute to a better understanding of the physiological roles of K_hib modification, and the K_hib proteome data will facilitate further investigations of the roles and mechanisms of K_hib modification in rhubarb.

SUBMITTER: Qi T

PROVIDER: S-EPMC8283887 | biostudies-literature |

REPOSITORIES: biostudies-literature

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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 surveyed the biological impact of 2-hydroxyisobutyrylation on lysine residuals (Khib) in C. albicans Using an antibody enrichment approach along with the traditional liquid chromatography-tandem mass spectrometry (LC-MS/MS) method, we analyzed the pattern of Khib-modified proteins and sites in one wild-type strain of C. albicans We identified 1,438 Khib-modified proteins with 6,659 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 compared with the reported numbers of lysine acetylation (Kac) and succinylation (Ksuc) sites, the numbers of 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. Findings in this study may provide new insights for studying posttranslational modification (PTM)-associated mechanisms in fungal development and pathogenicity.IMPORTANCEC. albicans is one of the most commonly reported fungal pathogens in mucosal and systemic infections. A better understanding of its growth habits and metabolic processes in the host should help improve defense strategies. The newly discovered protein posttranslational modification (PTM) on histones is one epigenetic mechanism which has been linked to many pathogenic events, including cancers. The types of PTM and their pathogenic roles in C. albicans are still somewhat poorly understood, even though studies of C. albicans based on acetylation inhibitors have shed some light on their function, and it seems that PTMs regulate pathogenic adhesion factors. Here, we quantified and analyzed the occurrence of lysine 2-hydroxyisobutyrylation (Khib) in C. albicans The Khib-modified proteins are enriched with respect to carbon metabolism, ribosomal biogenesis, and protein translation in C. albicans.

Project description:BackgroundLysine 2-hydroxyisobutyrylation (Khib) is a novel and conserved post-translational modification (PTM). Frankliniella occidentalis are economically important agricultural pests globally and also notorious for vectoring destructive plant viruses. To better study the disease transmission mechanism of F. occidentalis, it is necessary to conduct in-depth analysis of it. So far, no Khib modification of insects has been reported.ResultsIn this study, a proteome-wide analysis of Khib modifications in F. occidentalis was analyzed for the first time through the combination of high performance liquid chromatography fractionation technology and 2-hydroxyisobutyrylated peptide enrichment and other advanced technologies, 4093 Khib sites were identified on 1125 modified proteins. Bioinformatics and functional enrichment analyses showed that Khib-modified proteins were significantly enriched in many cell compartments and pathways, especially related to various cellular components and biological processes, and were more concentrated in ribosomes and proteasome subunits, involved in energy metabolism, protein synthesis and degradation, compared to the other nine species including Japonica rice, Homo sapiens, P. patens, Botrytis, Ustilaginoidea virens, Saccharomyces cerevisiae, T. gondii, C. albicans, and F. oxysporum. And Khib sites on virus-interacting insect proteins were discovered for the first time, such as cyclophilin and endoCP-GN.ConclusionsAfter three repeated experiments, we found a total of 4093 Khib sites on 1125 proteins. These modified proteins are mainly concentrated in ribosomes and proteasome subunits, and are widely involved in a variety of critical biological activities and metabolic processes of F. occidentalis. In addition, for the first time, Khib modification sites are found on the proteome of F. occidentalis, and these sites could be acted as for the virus interaction, including cyclophilin and endoCP-GN. The global map of 2-hydroxyisobutyrylation in thrips is an invaluable resource to better understand the biological processes of thrips and provide new means for disease control and mitigation of pest damage to crops.

Dataset Information

Global analysis of protein lysine 2-hydroxyisobutyrylation (K_hib) profiles in Chinese herb rhubarb (Dahuang).

Background

Results

Conclusions

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Dataset Information

Global analysis of protein lysine 2-hydroxyisobutyrylation (Khib) profiles in Chinese herb rhubarb (Dahuang).

Background

Results

Conclusions

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Global analysis of protein lysine 2-hydroxyisobutyrylation (K_hib) profiles in Chinese herb rhubarb (Dahuang).