Global Involvement of Lysine Crotonylation in Protein Modification and Transcription Regulation in Rice

Lysine crotonylation is a newly discovered post‐translational modification, which is structurally and functionally different from the widely studied lysine acetylation. Recent advances in the identification and quantification of lysine crotonylation by mass spectrometry have revealed that non‐histone proteins are frequently crotonylated, implicating it in many biological processes through the regulation of chromatin remodelling, metabolism, cell cycle and cellular organization. In this review, we summarize the writers, erasers and readers of lysine crotonylation, and their physiological functions, including gene transcription, acute kidney injury, spermatogenesis, depression, telomere maintenance, HIV latency and cancer process. These findings not only point to the new functions for lysine crotonylation, but also highlight the mechanisms by which crotonylation regulates various cellular processes.

Background: Low-temperature severely affects the growth and development of chrysanthemum which is one kind of ornamental plant well-known and widely used in the world. Lysine crotonylation is a recently identified post-translational modification (PTM) with multiple cellular functions. However, lysine crotonylation under low-temperature stress has not been studied. Results: Proteome-wide and lysine crotonylation of chrysanthemum at low temperature was analyzed using TMT labeling, sensitive immuno-precipitation, and high-resolution LC-MS/MS. The results showed that 2017 crotonylation sites were identified in 1199 proteins. Treatment at 4 °C for 24 h and −4 °C for 4 h resulted in 393 upregulated proteins and 500 downregulated proteins (1.2-fold threshold and P < 0.05). Analysis of biological information showed that lysine crotonylation was involved in photosynthesis, ribosomes, and antioxidant systems. The crotonylated proteins and motifs in chrysanthemum were compared with other plants to obtain orthologous proteins and conserved motifs. To further understand how lysine crotonylation at K136 affected APX (ascorbate eroxidase), we performed a site-directed mutation at K136 in APX. Site-directed crotonylation showed that lysine decrotonylation at K136 reduced APX activity, and lysine complete crotonylation at K136 increased APX activity. Conclusion: In summary, our study comparatively analyzed proteome-wide and crotonylation in chrysanthemum under low-temperature stress and provided insights into the mechanisms of crotonylation in positively regulated APX activity to reduce the oxidative damage caused by low-temperature stress. These data provided an important basis for studying crotonylation to regulate antioxidant enzyme activity in response to low-temperature stress and a new research ideas for chilling-tolerance and freezing-tolerance chrysanthemum molecular breeding.

Background: Lysine crotonylation is an important post-translational modification (PTM) process. Most research in this area has been carried out on mammals and yeast, but there has been no research published on crotonylated proteins on peanut.Results: In the current study, large-scale lysine crotonylation analysis was performed by a combination of affinity enrichment and high-resolution LC-MS/MS analysis. Altogether, 6051 lysine crotonylation sites were identified in 2508 protein groups. Bioinformatics analysis showed that lysine-crotonylated proteins were involved in many biological processes, such as carbon fixation in photosynthetic organisms, photosynthesis, biosynthesis of amino acids, ribosomes, etc. In particular, subcellular localization analysis showed that 43% of the crotonylated proteins were located in the chloroplast and that there were 29 crotonylated proteins associated with photosynthesis. In addition, 26 crotonylated proteins were identified in photosynthesis network and 145 proteins were mapped to ribosome network, indicating the diverse functions for lysine crotonylation in peanut.Conclusion: These data show that crotonylated proteins play a major part in peanut biological functions including carbon fixation in photosynthetic organisms, photosynthesis, biosynthesis of amino acids, ribosomes, etc. A lot of proteins related to photosynthesis and ribosome suggest that lysine crotonylation may play important regulatory roles in their structure and function. This dataset is the first comprehensive proteomics analysis of lysine crotonylation in peanut and will serve as an important resource with which to study the biosynthesis and function of lysine crotonylation in peanut and related plants. Based on these results, further studies to expand on the lysine crotonylation analysis were suggested. Data are available via ProteomeXchange with the identifier PXD017675.