Proteome-Wide Analysis of Lysine 2-Hydroxyisobutyrylation in the Phytopathogenic Fungus Botrytis cinerea

Abstract

Posttranslational modifications (PTMs) of the whole proteome have become a hot topic in the research field of epigenetics, and an increasing number of PTM types have been identified and shown to play significant roles in different cellular processes. Protein lysine 2-hydroxyisobutyrylation (Khib) is a newly detected PTM, and the 2-hydroxyisobutyrylome has been identified in several species. Botrytis cinerea is recognized as one of the most destructive pathogens due to its broad host distribution and very large economic losses; thus the many aspects of its pathogenesis have been continuously studied. However, distribution and function of Khib in this phytopathogenic fungus are not clear. In this study, a proteome-wide analysis of Khib in B. cinerea was performed, and 5,398 Khib sites on 1,181 proteins were identified. Bioinformatics analysis showed that the 2-hydroxyisobutyrylome in B. cinerea contains both conserved proteins and novel proteins when compared with Khib proteins in other species. Functional classification, functional enrichment and protein interaction network analyses showed that Khib proteins are widely distributed in cellular compartments and involved in diverse cellular processes. Significantly, 37 proteins involved in different aspects of regulating the pathogenicity of B. cinerea were detected as Khib proteins. Our results provide a comprehensive view of the 2-hydroxyisobutyrylome and lay a foundation for further studying the regulatory mechanism of Khib in both B. cinerea and other plant pathogens.

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

“…Khib is a newly discovered PTM reported in several species, such as mammals, plants, yeast, bacteria and fungi ( Huang et al, 2017 , 2018 ; Meng et al, 2017 ; Yin et al, 2019 ; Xu et al, 2020 ). In this research, Khib proteins were studied with proteome-wide analysis.…”

“…In U. virens , disruption of 2-hydroxyisobutyrylation in the MAPK pathway kinase UvSlt2 by mutation decreases fungal virulence ( Chen et al, 2021 ). In the comprehensive analysis of F. oxysporum , critical proteins for virulence – FoFmk1, FoHog1 and two MAP kinase signaling proteins – have been identified ( Qian et al, 2021 ); For B. cinerea , many 2-hydroxyisobutyrylated proteins are involved in substance synthesis and metabolism, redox and autophagy, kinase and protease, and are associated with the pathogenicity of B. cinerea ( Xu et al, 2020 ). However, similar studies on the peanut pathogen A. niger had not been reported.…”

“…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 ). Reports on these three pathogens have revealed that Khib is widely distributed in cellular compartments and is involved in diverse cellular processes, including regulation of pathogenicity and virulence.…”

Evidence for a synergistic effect of post‐translational modifications and genomic composition of eEF‐1α on the adaptation of Phytophthora infestans

“…These results further indicate that protein compositions, through their impacts on potential of PTMs such as protein ordering, could work together with genome structure to compensate for the evolutionary disadvantage of conserved genes such as eEF‐lα and other housekeeping genes in P. infestans in species. Indeed, it has been documented that protein disordering and many other PTMs can escalate the adaptation of species including pathogens to new environments independent of nucleotide variation (Brown et al., 2011; Nilsson et al., 2011; Volkwein et al., 2019; Xu et al., 2020; Yang et al, 2020).…”

Quantitative multiplexed proteomics analysis reveals reshaping of the lysine 2-hydroxyisobutyrylome in Fusarium graminearum by tebuconazole

“…Recent studies have shown that this modification is evolutionarily conserved across bacteria, yeast, plants, animals, and humans on both histone and nonhistone proteins [1][2][3][4][5][6][7]. Recently, the 2-hydroxyisobutyrylomes of three filamentous fungi, namely, Ustilaginoidea virens, Botrytis cinerea, and Fusarium oxysporum, were also reported [8][9][10]. Khib adds a large 2-hydroxyisobutyryl group to the lysine residue, which increases the size of the lysine side chain, abolishes the positive charge, and introduces a hydroxyl group that enables the modified lysine to form hydrogen bonds with other molecules [1].…”