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Table 3 Global profiling of non-histone crotonylation based on LC–MS/MS analysis

From: Emerging roles of non-histone protein crotonylation in biomedicine

Biological samples analyzed Experiment condition Identified proteins Kcr sites Amino acids flanking the identified Kcr sites Subcellular localization Biological function Validated proteins by WB Year References
H. sapiens
 IgAN patients PBMCs were obtained and compared with normal controls 353 770 Alanine (A), aspartic acid (D), and lysine (K) residues at the − 1 to + 1 positions Organelles, extracellular regions and membranes (69%) Upregulated proteins involved: focal adhesion, cell-substrate junction, cell-substrate adherens junction, biological process of regulation of body fluid levels, and calcium ion binding.Downregulated proteins involved: cellular component of blood microparticle, biological process of humoral immune response, and ubiquitin-like protein ligase binding N/A 2020 [68]
 HeLa cells CDYL KO 3734 14,311 Negatively charged glutamic acid (E) at − 1 and + 1 positions Mitochondria (18%), cytoplasm and nucleus (roughly equal) Translation initiation, RNA splicing, and amino acid metabolism RPA1, APEX1, and HP1 2020 [52]
 HCT116 cells P300 KO 392 816 Glutamic acid (E) at − 4, − 1, + 1, and + 4 positions, valine(V) at + 2 position Nucleus (69%), cytosol (89%), and mitochondria (19%) Co-translational protein targeting to membrane, nuclear-transcribed mRNA catabolic process, and translational initiation LMNB2 2018 [61]
 PBMCs of patients with hemodialysis maintenance PBMCs were obtained and compared with normal controls 347 1109 Aspartic acid (D) and glutamine (E) at − 1 to + 4 position; lysine (K) at − 10 to − 5 and + 10 to + 5 positions Upregulated crotonylated proteins: cytoplasm (46%), nucleus (14%), mitochondria (12%), and extracellular region (11%). Downregulated proteins: cytoplasm (57%), extracellular region (11%), mitochondria (9%), and nucleus (8%) Upregulated proteins enriched in cellular metabolic process and cellular response to outside and downregulated proteins localized in cellular functions such as migration and development N/A 2018 [56]
 H1299 cells Without any treatment 1024 2696 Glutamate (E) residues at the − 1 and + 1 positions Cytoplasm (40%), nucleus (27%), and mitochondria (13%) 18% of crotonylated proteins are involved in the cell process, 14% are involved in metabolism, 13% are single biological proteins, and 11% are biomodulatory proteins NPM1, FHL1, ACTN1, Integrin β1, Vinculin, ERK2, CDK1, GAPDH, and OTUB1 2017 [17]
 HeLa cells Treated with NaCr 453 558 Alanine (A) residues at + 3 or − 6 positions Nuclear proteins (62.3%), nucleoplasmic localization proteins (9.4%), other cellular components including plasma membrane, cytoplasm, Golgi apparatus, and unclassified proteins (28.3%) RNA processing, nucleic acid metabolism, chromosome organization, gene expression, DNA conformational change and packaging, chromatin organization and cell cycle CBX3, CBX5、MTA2, Cul4B, and HDAC1 2017 [49]
Without any treatment 70 N/A N/A N/A Various molecular functions and biological processes closely related to DNA and RNA metabolism and cell cycle HDAC1 2017 [49]
 A549 cells Treated with SAHA 2021 8475 N/A Cytoplasm (35.7%), nucleus (27.4%) and mitochondria (13.5%) Gene expression, transcription, protein folding, and a variety of metabolic processes N/A 2017 [21]
Others
 T. gondii RH strain 3735 1,061 Isoleucine (I) and lysine (K) occurred upstream; leucine (L), lysine (K) and phenylalanine (F) occurred downstream Concentrated in and around the nucleus Related to protein translation, compound metabolism, and biosynthesis N/A 2019 [71]
ME49 strain 3396 984
 The tea plants NH4 + deficiency/resupply 971 2288 Alanine (A), glutamate (E), and lysine (K) residues at surrounding positions Chloroplast (36.8%), cytoplasm (33.0%), and nucleus (13.7%) Photosynthesis, carbon fixation, and amino acid metabolism N/A 2019 [60]
 Oryza sativa L. japonica Without any treatment 690 1265 Aspartic acid (D), glutamine (E), isoleucine (I), lysine (K), leucine (L), arginine (R), and valine (V) at surrounding positions Chloroplast (51%), cytoskeleton (1%), endoplasmic reticulum (1%), and extracellularly located (2%) Photosynthesis N/A 2018 [70]
 Carica papaya L. Without any treatment 2120 5995 Alanine (A), aspartic acid (D), and glutamine (E) at − 5 to − 1 and + 1 to + 5 positions, while lysine(K) and arginine (R) at − 10 to − 5 and + 5 to + 10 positions Chloroplast (713 peptides), cytosol (691 peptides), nucleus (290 peptides), and mitochondria (138 peptides) Biosynthesis of antibiotics, carbon metabolism, biosynthesis of amino acids, and glycolysis N/A 2018 [69]
 Zebrafish embryos Without any treatment 218 557 Hydrophobic (L, I, V) and acidic (D and E) amino acids at surrounding positions Cytosol (58%), mitochondria (11%), extracellular matrix (8%), and plasma membrane (6%) Translation, metabolic process, and diverse regulation of skeletal muscle contraction N/A 2018 [18]
 PAT Degradation in Rhodotorula mucilaginosa 629 1691 Negatively charged residues from − 10 to + 10 Mitochondria (39%), cytosol (32%), and nucleus (14%) Metabolic process, cellular process, and single-organism process with upregulated or downregulated proteins N/A 2018 [54]
 Nicotiana tabacum Without any treatment 637 2044 Aspartic acid (D) and glutamine (E), at surrounding positions Chloroplast (37%), cytosol (30%), nucleus (12%), and mitochondria (5%) Carbon metabolism, the citrate cycle, glycolysis, and photosynthesis the biosynthesis of amino acids N/A 2017 [25]
  1. A549 human lung adenocarcinoma cells, CDYL chromodomain Y-like protein, HCT116 human colon cancer cells, HeLa human cervical adenocarcinoma cells, H1299 human lung adenocarcinoma cells, IgAN immunoglobulin A nephropathy, KO knockout, NaCr sodium crotonate N/A not available, PAT patulin, PBMCs peripheral blood mononuclear cells, SAHA suberoylanilide hydroxamic acid, T. gondii toxoplasma gondii parasites