Advances in proteome-wide analysis of plant lysine acetylation

Xia, Linchao; Kong, Xiangge; Song, Haifeng; Han, Qingquan; Zhang, Sheng

doi:10.1016/j.xplc.2021.100266

Cited by 25 publications

(15 citation statements)

References 154 publications

(351 reference statements)

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“…Four histone proteins, including two histone H2A (Cd4A1G007030.1 and Cd4A1G023750.1), one histone H2B (Cd2A2G026820.1) and one histone 4 (Cd7A1G012090.1), are known to participate in gene expression regulation in plant growth and development (Fig. S 6 ; Table S 10 ) [ 43 ]. Acetylation of the four histone proteins at conserved lysine sites might be important for fast organ growth in the three grasses; however, the detailed regulatory functions of other conserved acetylated and succinylated proteins are unclear.…”

Section: Resultsmentioning

confidence: 99%

“…Our analyses successfully identified thousands of lysine acetylation modifications and hundreds of lysine succinylation modifications in fast-growing stolons of bermudagrass, however, many acetylated proteins and succinylated proteins possibly having important functions might not be determined due to their low abundance or poor reactivity with the affinity antibodies [ 43 ]. On the other hand, many studies have revealed that both acetylation and succinylation modifications exist in very low stoichiometries [ 5 , 59 – 61 ].…”

Section: Discussionmentioning

confidence: 99%

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Proteome-wide analyses reveal diverse functions of protein acetylation and succinylation modifications in fast growing stolons of bermudagrass (Cynodon dactylon L.)

et al. 2022

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Background Bermudagrass (Cynodon dactylon L.) is an important warm-season turfgrass species with well-developed stolons, which lay the foundation for the fast propagation of bermudagrass plants through asexual clonal growth. However, the growth and development of bermudagrass stolons are still poorly understood at the molecular level. Results In this study, we comprehensively analyzed the acetylation and succinylation modifications of proteins in fast-growing stolons of the bermudagrass cultivar Yangjiang. A total of 4657 lysine acetylation sites on 1914 proteins and 226 lysine succinylation sites on 128 proteins were successfully identified using liquid chromatography coupled to tandem mass spectrometry, respectively. Furthermore, 78 proteins and 81 lysine sites were found to be both acetylated and succinylated. Functional enrichment analysis revealed that acetylated proteins regulate diverse reactions of carbohydrate metabolism and protein turnover, whereas succinylated proteins mainly regulate the citrate cycle. These results partly explained the different growth disturbances of bermudagrass stolons under treatment with sodium butyrate and sodium malonate, which interfere with protein acetylation and succinylation, respectively. Moreover, 140 acetylated proteins and 42 succinylated proteins were further characterized having similarly modified orthologs in other grass species. Site-specific mutations combined with enzymatic activity assays indicated that the conserved acetylation of catalase and succinylation of malate dehydrogenase both inhibited their activities, further implying important regulatory roles of the two modifications. Conclusion In summary, our study implied that lysine acetylation and succinylation of proteins possibly play important regulatory roles in the fast growth of bermudagrass stolons. The results not only provide new insights into clonal growth of bermudagrass but also offer a rich resource for functional analyses of protein lysine acetylation and succinylation in plants.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Proteome-wide analyses reveal diverse functions of protein acetylation and succinylation modifications in fast growing stolons of bermudagrass (Cynodon dactylon L.)

et al. 2022

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“…These have revealed a large number of potential key regulators of Pi homeostasis in plants, especially in Arabidopsis thaliana ( Thibaud et al, 2010 ; Woo et al, 2012 ) and rice ( Secco et al, 2013 ; Gho et al, 2018 ). Protein phosphorylation and succinylation are the two most important PTMs for regulating multiple biological processes in plants ( Nakagami et al, 2010 ; Xia et al, 2022 ). The recent developments of high-resolution mass spectrometry, antibody based affinity enrichment proteomic technology, and powerful bioinformatic tools have substantially contributed to the global analysis of protein phosphorylation and succinylation in barley.…”

Section: Discussionmentioning

confidence: 99%

Global proteome analyses of phosphorylation and succinylation of barley root proteins in response to phosphate starvation and recovery

Wang

Li²,

Yao³

et al. 2022

Front. Plant Sci.

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Phosphate (Pi) stress is an important environmental factor that limits plant growth and development. Of various posttranslational modifications (PTMs), protein phosphorylation and succinylation are the two most important PTMs that regulate multiple biological processes in response to Pi stress. However, these PTMs have been investigated individually but their interactions with proteins in response to Pi stress remain poorly understood. In this study, to elucidate the underlying mechanisms of protein phosphorylation and succinylation in response to Pi stress, we performed a global analysis of the barley root phosphorylome and succinylome in Pi starvation and recovery stages, respectively. A total of 3,634 and 884 unique phosphorylated and succinylated proteins, respectively, corresponding to 11,538 and 2,840 phospho- and succinyl-sites, were identified; of these, 275 proteins were found to be simultaneously phosphorylated and succinylated. Gene Set Enrichment Analysis was performed with a Kyoto Encyclopedia of Genes and Genomes pathway database revealing pathways that significantly enriched in the phosphorylome and succinylome. Such pathways, were dynamically regulated by Pi starvation and recovery treatments, and could be partitioned into distinct metabolic processes. In particular, phosphorylated proteins related to purine, the mitogen-activated protein kinase (MAPK) signaling pathway, pyrimidine, and ATP-binding cassette (ABC) transporters were upregulated in both Pi deprivation and recovery stages. Succinylated proteins, significantly upregulated by both Pi starvation and recovery, were enriched in nitrogen metabolism and phenylpropanoid biosynthesis. Meanwhile, succinylated proteins that were significantly downregulated by both Pi starvation and recovery were enriched in lysine degradation and tryptophan metabolism. This highlighted the importance of these metabolic pathways in regulating Pi homeostasis. Furthermore, protein–protein interaction network analyses showed that the response of central metabolic pathways to Pi starvation and recovery was significantly modulated by phosphorylation or succinylation, both individually and together. In addition, we discovered relevant proteins involved in MAPK signaling and phenylpropanoid biosynthetic pathways existing in interactions between phosphorylated and succinylated proteins in response to Pi recovery. The current study not only provides a comprehensive analysis of phosphorylated and succinylated proteins in plant responses to Pi starvation and recovery, but also reveals detailed interactions between phosphorylated and succinylated proteins in barley roots.

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“…Protein acetylation is a ubiquitous PTM, found in both eukaryotes and prokaryotes, and is involved in various key cellular processes [ 3 , 69 ]. Expression, biosynthesis and secretion of pathogenic factors in pathogens are regulated by protein acetylation during the interaction between pathogens and host plants [ 70 ].…”

Section: Discussionmentioning

confidence: 99%

“…Lysine-ε-acetylation (Kac) is a conserved post-translational modification (PTM) that was first discovered on histone proteins in 1964 [ 1 ], and occurs widely on non-histone in distinct organisms [ 2 , 3 ]. A few studies showed that Kac of non-histone is involved in the regulation of a range of biological processes [ 4 ].…”

Section: Introductionmentioning

confidence: 99%

A comprehensive dynamic immune acetylproteomics profiling induced by Puccinia polysora in maize

Deng

Ding

et al. 2022

BMC Plant Biol

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Lysine-ε-acetylation (Kac) is a reversible post-translational modification that plays important roles during plant-pathogen interactions. Some pathogens can deliver secreted effectors encoding acetyltransferases or deacetylases into host cell to directly modify acetylation of host proteins. However, the function of these acetylated host proteins in plant-pathogen defense remains to be determined. Employing high-resolution tandem mass spectrometry, we analyzed protein abundance and lysine acetylation changes in maize infected with Puccinia polysora (P. polysora) at 0 h, 12 h, 24 h, 48 h and 72 h. A total of 7412 Kac sites from 4697 proteins were identified, and 1732 Kac sites from 1006 proteins were quantified. Analyzed the features of lysine acetylation, we found that Kac is ubiquitous in cellular compartments and preferentially targets lysine residues in the -F/W/Y-X-X-K (ac)-N/S/T/P/Y/G- motif of the protein, this Kac motif contained proteins enriched in basic metabolism and defense-associated pathways during fungal infection. Further analysis of acetylproteomics data indicated that maize regulates cellular processes in response to P. polysora infection by altering Kac levels of histones and non-histones. In addition, acetylation of pathogen defense-related proteins presented converse patterns in signaling transduction, defense response, cell wall fortification, ROS scavenging, redox reaction and proteostasis. Our results provide informative resources for studying protein acetylation in plant-pathogen interactions, not only greatly extending the understanding on the roles of acetylation in vivo, but also providing a comprehensive dynamic pattern of Kac modifications in the process of plant immune response.

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Advances in proteome-wide analysis of plant lysine acetylation

Cited by 25 publications

References 154 publications

Proteome-wide analyses reveal diverse functions of protein acetylation and succinylation modifications in fast growing stolons of bermudagrass (Cynodon dactylon L.)

Proteome-wide analyses reveal diverse functions of protein acetylation and succinylation modifications in fast growing stolons of bermudagrass (Cynodon dactylon L.)

Global proteome analyses of phosphorylation and succinylation of barley root proteins in response to phosphate starvation and recovery

A comprehensive dynamic immune acetylproteomics profiling induced by Puccinia polysora in maize

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