Global analysis of lysine 2-hydroxyisobutyrylation in wheat root

Abstract

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. 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.

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

“…To enrich peptides, we incubated tryptic peptides dissolved in NETN buffer (100 mM NaCl, 1 mM EDTA, 50 mM Tris–HCl, and 0.5% NP-40, pH 8.0) with pre-washed agarose-conjugated anti Khib antibody beads (Micrometer Biotech, Hangzhou, China) at 4°C overnight with gentle shaking ( Bo et al, 2021 ). The beads were washed four times with NETN buffer and twice with ddH 2 O.…”

“…To date, Khib has been reported in several species, as described in the first report of global profiling of the Khib proteome in mammalian cells, which discovered both the “writers” and “erasers” of histone Khib marks and major Khib protein substrates ( Huang et al, 2018 ). Large amounts of Khib have been reported in plants, such as developing rice seeds ( Meng et al, 2017 ), common wheat ( Bo et al, 2021 ; Zhang et al, 2021 ) and Physcomitrella patens ( Yu et al, 2017 ); Histone H4K8 2-hydroxyisobutyrylation (H4K8 hib) has been identified as an evolutionarily conserved modification in Saccharomyces cerevisiae ( Huang et al, 2017 ). Some reports have described Khib in biological pathogens, such as the animal pathogens Proteus mirabilis , Toxoplasma gondii , and Candida albicans ( Dong et al, 2018 ; Yin et al, 2019 ; Zheng et al, 2021 ), Khib in plant pathogens has also been reported, such as Fusarium oxysporum , Botrytis cinerea , and Ustilaginoidea virens ( Xu et al, 2020 ; Chen et al, 2021 ; Qian et al, 2021 ).…”

Global analysis of lysine 2-hydroxyisobutyrylation during Fusarium graminearum infection in maize

“…Lysine 2-hydroxyisobutyrylation (Khib) on histones is widespread in plants, such as Arabidopsis , rice, Physcomitrella patens , and wheat ( Meng et al, 2017 ; Xue et al, 2020 ; Bo et al, 2021 ; Zhang et al, 2021 ). However, Khib modification on histones in maize had not been identified.…”

“…Proteome-wide identification and properties of Khib sites in maize. Frontiers in Plant Science 06 frontiersin.org Bo et al, 2021;Zhang et al, 2021). However, Khib modification on histones in maize had not been identified.…”

“…In rice, 9,916 Khib modification sites are identified on 2,512 proteins in seeds, while 4,163 Khib sites are identified on 1,596 proteins of rice seedlings, which were involved in a variety of biological functions and metabolic processes ( Meng et al, 2017 ; Xue et al, 2020 ). In wheat, 1,074 proteins are identified by proteomics technology, including 3,348 Khib lysine modification sites, and the key regulation of Khib modification of K206 on PGK on enzyme activity is proved ( Bo et al, 2021 ; Zhang et al, 2021 ). Total of 1,525 proteins with 4,333 Khib-modified peptides are identified in Chinese herb rhubarb ( Qi et al, 2021 ).…”