• Molecules and Cells
• /
• 제45권3호
• /
• pp.158-167
• /
• 2022

Ubiquitin (Ub) is post-translationally modified by Ub itself or Ub-like proteins, phosphorylation, and acetylation, among others, which elicits a variety of Ub topologies and cellular functions. However, N-terminal (Nt) modifications of Ub remain unknown, except the linear head-to-tail ubiquitylation via Nt-Met. Here, using the yeast Saccharomyces cerevisiae and an Nt-arginylated Ub-specific antibody, we found that the detectable level of Ub undergoes Nt-Met excision, Nt-deamination, and Nt-arginylation. The resulting Nt-arginylated Ub and its conjugated proteins are upregulated in the stationary-growth phase or by oxidative stress. We further proved the existence of Nt-arginylated Ub in vivo and identified Nt-arginylated Ub-protein conjugates using stable isotope labeling by amino acids in cell culture (SILAC)-based tandem mass spectrometry. In silico structural modeling of Nt-arginylated Ub predicted that Nt-Arg flexibly protrudes from the surface of the Ub, thereby most likely providing a docking site for the factors that recognize it. Collectively, these results reveal unprecedented Nt-arginylated Ub and the pathway by which it is produced, which greatly expands the known complexity of the Ub code.

• Molecules and Cells
• /
• 제40권7호
• /
• pp.441-449
• /
• 2017

Proteolysis in eukaryotic cells is mainly mediated by the ubiquitin (Ub)-proteasome system (UPS) and the autophagy-lysosome system (hereafter autophagy). The UPS is a selective proteolytic system in which substrates are recognized and tagged with ubiquitin for processive degradation by the proteasome. Autophagy is a bulk degradative system that uses lysosomal hydrolases to degrade proteins as well as various other cellular constituents. Since the inception of their discoveries, the UPS and autophagy were thought to be independent of each other in components, action mechanisms, and substrate selectivity. Recent studies suggest that cells operate a single proteolytic network comprising of the UPS and autophagy that share notable similarity in many aspects and functionally cooperate with each other to maintain proteostasis. In this review, we discuss the mechanisms underlying the crosstalk and interplay between the UPS and autophagy, with an emphasis on substrate selectivity and compensatory regulation under cellular stresses.

• Molecules and Cells
• /
• 제22권3호
• /
• pp.247-253
• /
• 2006

Protein modification by small ubiquitin-like modifier (SUMO) controls diverse cellular functions of protein targets including transcription factors and coregulators mainly in the nucleus and participates in maintaining cellular homeostasis. In addition, SUMO system plays important roles in DNA damage repair and maintaining genome integrity. Thus, in some cases, the loss of control on SUMOylation or deSUMOylation processes causes a defect in maintaining homeostasis and hence gives a cue to cancer development. Furthermore, recent study showed that SUMO system is also involved in cancer metastasis. In this review, we will summarize and discuss the possible role of SUMO system in cancer development and metastasis.

• Bulletin of the Korean Chemical Society
• /
• 제30권9호
• /
• pp.2061-2065
• /
• 2009

Two simple algorithm modifications are made to the THRASH data retrieval program with the aim of improving analysis speed for complex Fourier transform ion cyclotron resonance (FTICR) mass spectra. Instead of calculating the least-squares fit for every charge state in the backup charge state determination algorithm, only some charge states are pre-selected based on the plausibility values obtained from the FT/Patterson analysis. Second, a modification is made to skip figure-of-merit (FOM) calculations in the central m/z region between two neighboring peaks in isotopic cluster distributions, in which signal intensities are negligible. These combined modifications result in a significant improvement in the analysis speed, which reduces analysis time as much as 50% for ubiquitin (8.6 kDa, 76 amino acids) FTICR MS and MS/MS spectra at the reliability (RL) value = 0.90 and five pre-selected charge states with minimal decreases in data analysis quality (Table 3).