Several important proteins involved in DNA repair pathway such as Mdc1, Trp53bp1 and H2ax were recognized in our study

Several important proteins involved in DNA repair pathway such as Mdc1, Trp53bp1 and H2ax were recognized in our study. whereas SUMO2 and SUMO3 are each 45% identical to SUMO1. SUMOylation is a covalent, reversible modification TAS-114 that can add one of three SUMO proteins to lysines on target proteins. Similar to ubiquitination, the conjugation of mammalian SUMO to protein substrates requires the E1 activating enzyme (SAE1/SAE2), E2 conjugase (Ubc9), and, in some cases, E3 ligases (1,2). SUMO proteins can be deconjugated from substrates via the Sentrin-specific proteases (SENPs). Six mammalian SENPs exist,i.e.SENP1, SENP2, SENP3, SENP5, SENP6, and SENP7 (3). Protein SUMOylation is associated with many fundamental pathways in both nucleus and cytoplasm including nuclear transport, transcription regulation, DNA replication, DNA repair, genome stability, and cell cycle Rabbit Polyclonal to GSK3alpha (phospho-Ser21) progression (1,4,5). Ubc9 catalyzes the formation of an isopeptide bond between the C-terminal glycine of SUMOs 13 and an -amino group of the target lysine by direct interaction with a typical consensus motif KxE/D (where is usually a large hydrophobic amino acid residue andxis any residue) present in protein substrates (6,7). However, many SUMOylation sites remain in nonconsensus motif, such as Lys164of PCNA (8,9). Therefore, bioinformatics prediction for SUMOylation sites is not sufficiently accurate. An in-depth understanding of SUMOylation by the direct identification of endogenous SUMO sites at the proteome level is essential for accessing its physiological and pathological functions. By using proteomic strategies, experts can identify the global SUMOylation proteome through the purification of SUMOylated targets. However, the low large quantity of SUMOylated proteins and dynamic nature of this modification hinder the large-scale identification of protein SUMOylation and mapping of SUMOylated sites by mass spectrometry (MS) in mammalian cells. In addition, after trypsin digestion, mammalian SUMO paralogs remain a relatively long remnant TAS-114 peptide (19 and 32 amino acids, TAS-114 respectively, for mammalian SUMO1 and SUMO2/3), which leads to complex MS/MS fragmentation ion patterns. Consequently, the subsequent MS identification becomes challenging. To this end, great efforts have been made in recent years to develop methods of identifying SUMOylation sites. Previous studies have developed a strategy of overexpressing tagged SUMO plasmids with mutation, such as TGG/RGG, to facilitate the MS identification of SUMO-modified sites. With the aid of affinity purification, tagged SUMO has been successfully used to identify SUMO targets on a global level (1024). Vertegaal’s group used a similar approach to map SUMO2/3-altered sites (25) and recognized over 4300 SUMOylation sites (21). Hay RT’s group launched K–GG antibody into SUMO proteome research and eventually mapped 1002 SUMO2-altered sites (22). Although purification strategies with tagged SUMO have been successfully used to identify SUMO targets on a TAS-114 global level, this approach is usually confined to cells and genetically designed organism applications, thereby providing limited insight into the endogenous regulation of target SUMOylation. In order to get deeper insights into the physiological function of SUMO modification, some experts have begun to focus on the study of endogenous TAS-114 SUMO modification. Beckeret al.(26) have developed a protocol that can enable the enrichment of endogenously SUMOylated proteins but cannot identify SUMOylation sites. To date, there are limited methods that can directly identify endogenous SUMOylation sites. Hendrikset al.generated an approach named PRISM (Protease-Reliant Identification of SUMO Modification), which can be successfully used to identify modification sites of wild-type SUMO (27). However, they still analyzed overexpressed His-tagged SUMO rather than endogenous SUMO, because this approach did not solve the problem of endogenous SUMOylated protein/peptide enrichment. So far, there is still no method for both endogenous wild-type SUMOylated peptides purification and SUMOylation sites identification. In the present study, we generated a pan-SUMO1 antibody specific to the C-terminal of SUMO1 remnant. Using a dual-high-resolution MS platform, we recognized 53 high-confidence endogenous SUMO1-altered sites from mouse testis. The enrichment of modification sequence confirmed the consensus KxE motif observed in previous functional.