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As predicted by systems biology, a paradigm shift will emerge through the integration of information about different layers of cellular processes. The cell cycle network is at the heart of the cellular computing system, and orchestrates versatile cellular functions. The NIRF/UHRF2 ubiquitin ligase is an "intermodular hub" that occupies a central position in the network, and facilitates coordination among the cell cycle machinery, the ubiquitin-proteasome system, and the epigenetic system. NIRF interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. NIRF ubiquitinates cyclins D1 and E1, and induces G1 arrest. The NIRF gene is frequently lost in tumors and is a candidate tumor suppressor, while its paralog, the UHRF1 gene, is hardly altered. Thus, investigations of NIRF are essential to understand the entire biological systems. Through integration of the enormous information flows, NIRF may contribute to the coupling between the cell cycle network and the epigenetic landscape. We propose the new paradigm that NIRF produces the extreme diversity in the network wiring that helps the diversity of Waddington's canals.
ARMET is an endoplasmic reticulum (ER) stress-inducible protein that is required for maintaining cell viability under ER stress conditions. However, the exact molecular mechanisms by which ARMET protects cells are unknown. Here, we have analyzed the solution structure of ARMET. ARMET has an entirely alpha-helical structure, which is composed of two distinct domains. Positive charges are dispersed on the surfaces of both domains and across a linker structure. Trypsin digestion and (15)N relaxation experiments indicate that the tumbling of the N-terminal and C-terminal domains is effectively independent. These results suggest that ARMET may hold a negatively charged molecule using the two positively charged domains.
Ataxin-3, which is encoded by a gene that has been associated with Machado-Joseph disease, contains a catalytic N-terminal Josephin domain with deubiquitinase activity. Here, we show that the Josephin domain of ataxin 3 catalyzes endo-type cleavage of Lys48-linked polyubiquitin. Furthermore, NMR data obtained following site-specific paramagnetic spin labeling of Lys48-linked di-ubiquitin revealed that both ubiquitin units interact with the Josephin domain, with the C-terminal Gly76 of the proximal unit being situated in the vicinity of the catalytic triad of Josephin domain. Our results help to elucidate how the substrate is recognized by the Josephin domain and properly positioned for an endo-type deubiquitination reaction.
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