First comprehensive analysis of lysine succinylation in paper mulberry (Broussonetia papyrifera)

Abstract

Background Lysine succinylation is a naturally occurring post-translational modification (PTM) that is ubiquitous in organisms. Lysine succinylation plays important roles in regulating protein structure and function as well as cellular metabolism. Global lysine succinylation at the proteomic level has been identified in a variety of species; however, limited information on lysine succinylation in plant species, especially paper mulberry, is available. Paper mulberry is not only an important plant in traditional Chinese medicine, but it is also a tree species with significant economic value. Paper mulberry is found in the temperate and tropical zones of China. The present study analyzed the effects of lysine succinylation on the growth, development, and physiology of paper mulberry. Results A total of 2097 lysine succinylation sites were identified in 935 proteins associated with the citric acid cycle (TCA cycle), glyoxylic acid and dicarboxylic acid metabolism, ribosomes and oxidative phosphorylation; these pathways play a role in carbon fixation in photosynthetic organisms and may be regulated by lysine succinylation. The modified proteins were distributed in multiple subcellular compartments and were involved in a wide variety of biological processes, such as photosynthesis and the Calvin-Benson cycle. Conclusion Lysine-succinylated proteins may play key regulatory roles in metabolism, primarily in photosynthesis and oxidative phosphorylation, as well as in many other cellular processes. In addition to the large number of succinylated proteins associated with photosynthesis and oxidative phosphorylation, some proteins associated with the TCA cycle are succinylated. Our study can serve as a reference for further proteomics studies of the downstream effects of succinylation on the physiology and biochemistry of paper mulberry.

Quantitative Succinyl-Proteome Profiling of Turnip (Brassica rapa var. rapa) in Response to Cadmium Stress

“…However, the global succinyl-proteome characteristics showed some similarity between turnip and other species. For example, the number of succinylated sites per protein was negatively correlated with the corresponding protein number in turnip ( Figure 2 B), which is consistent with the results in Broussonetia papyrifera [ 22 ]. Among these succinylated proteins, RuBisCO and dihydrolipoyl dehydrogenase contained as many as 13 succinylated sites ( Table S1, Supplementary Materials ).…”

“…In contrast to previous studies [ 19 , 22 , 38 ], no consensus sequence motif was extracted from the succinylated proteins in this study, which may be attributed to multiple reasons. However, the main over-represented amino acids (i.e., glycine and alanine) surrounding the succinylated lysine sites in the turnip shoots ( Figure S5, Supplementary Materials ) were consistent with other species [ 22 , 38 ], which may be because these amino acids (e.g., glycine and alanine), with relatively weak steric hindrance effects, are more compatible with succinyl groups [ 38 ]. The results indicate the specific and common lysine succinylation characteristics in turnip seedlings compared to other species.…”

“…The protein extraction was conducted according to previous studies with some modifications [ 22 , 23 ]. In brief, the shoot samples of turnip plants collected at different time points were first ground with liquid nitrogen, then the powders were transferred to a 5 mL centrifuge tube and sonicated three times on ice using a high intensity ultrasonic processor (Scientz) in lysis buffer [ 22 ].…”

“…The protein extraction was conducted according to previous studies with some modifications [ 22 , 23 ]. In brief, the shoot samples of turnip plants collected at different time points were first ground with liquid nitrogen, then the powders were transferred to a 5 mL centrifuge tube and sonicated three times on ice using a high intensity ultrasonic processor (Scientz) in lysis buffer [ 22 ]. Equal volumes of Tris-saturated phenol (pH 8.0) were added and then the mixtures were further vortexed for 5 min, after centrifugation (5000× g , 4 °C, 10 min), the upper phenol phases were transferred to a new centrifuge tube.…”

“…Based on the WB results, quantitative succinyl-proteome profiling was performed to understand the potential mechanisms of the turnip response to Cd. The main experimental and analytical processes ( Figure S1, Supplementary Materials ), including trypsin digestion, succinylation modification enrichment, liquid chromatography–mass spectrometry (LC–MS) analysis, database searching, motif analysis, and protein function annotation, were performed using previously described methods [ 22 , 23 , 25 , 26 ].…”