A Role for USP7 in DNA Replication

The minichromosome maintenance (MCM) complex, which plays multiple important roles in DNA replication, is loaded onto chromatin following mitosis, remains on chromatin until the completion of DNA synthesis, and then is unloaded by a poorly defined mechanism that involves the MCM binding protein (MCM-BP). Here we show that MCM-BP directly interacts with the ubiquitin-specific protease USP7, that this interaction occurs predominantly on chromatin, and that MCM-BP can tether USP7 to MCM proteins. Detailed biochemical and structure analyses of the USP7–MCM-BP interaction showed that the ¹⁵⁵PSTS¹⁵⁸ MCM-BP sequence mediates critical interactions with the TRAF domain binding pocket of USP7. Analysis of the effects of USP7 knockout on DNA replication revealed that lack of USP7 results in slowed progression through late S phase without globally affecting the fork rate or origin usage. Lack of USP7 also resulted in increased levels of MCM proteins on chromatin, and investigation of the cause of this increase revealed a defect in the dissociation of MCM proteins from chromatin in mid- to late S phase. This role of USP7 mirrors the previously described role for MCM-BP in MCM complex unloading and suggests that USP7 works with MCM-BP to unload MCM complexes from chromatin at the end of S phase.     

Further Insight into Substrate Recognition by USP7: Structural and Biochemical Analysis of the HdmX and Hdm2 Interactions with USP7

Ubiquitin-specific protease 7 (USP7) catalyzes the deubiquitination of several substrate proteins including p53 and Hdm2. We have previously shown that USP7, and more specifically its amino-terminal domain (USP7-NTD), interacts with distinct regions on p53 and Hdm2 containing P/AxxS motifs. The ability of USP7 to also deubiquitinate and control the turnover of HdmX was recently demonstrated. We utilized a combination of biochemistry and structural biology to identify which domain of USP7 interacts with HdmX as well as to identify regions of HdmX that interact with USP7. We showed that USP7-NTD recognized two of six P/AxxS motifs of HdmX (⁸AQCS¹¹ and ³⁹⁸AHSS⁴⁰¹). The crystal structure of the USP7-NTD:HdmX^AHSS complex was determined providing the molecular basis of complex formation between USP7-NTD and the HdmX^AHSS peptide. The HdmX peptide interacted within the same residues of USP7-NTD as previously demonstrated with p53, Hdm2, and EBNA1 peptides. We also identified an additional site on Hdm2 (³⁹⁷PSTS⁴⁰⁰) that interacts with USP7-NTD and determined the crystal structure of this complex. Finally, analysis of USP7-interacting peptides on filter arrays confirmed the importance of the serine residue at the fourth position for the USP7-NTD interaction and showed that phosphorylation of serines within the binding sequence prevents this interaction. These results lead to a better understanding of the mechanism of substrate recognition by USP7-NTD.     

Adaptive changes in NAD+ metabolism in ultraviolet light-irradiated murine lymphoma cells

We have determined the ability of UV_254nm-irradiated murine lymphoma cells to adapt their NAD⁺ metabolism to the increased NAD⁺ consumption for the poly ADP-ribosylation of chromatin proteins. Two murine lymphoma sublines with differential UV-sensitivity and poly(ADP-ribose) turnover were used as a model system. The first subline, designated LY-R is UV_254nm-sensitive and tumorigenic in DBA/2 mice. The second subline, LY-S is UV_254nm-resistant and nontumorigenic. Following treatment of these cells with 2 mM benzamide, an inhibitor of the NAD⁺-utilizing enzyme poly(ADP-ribose) polymerase, NAD⁺ levels slowly increased up to about 160% of control levels after 3 hours. When benzamide was added to these cultures 20 min after UV_254nm irradiation, a dramatic transient increase of NAD⁺ levels was observed within 4 min in LY-R cells and more moderately in LY-S cells. At later times after UV_254nm irradiation, the NAD⁺ levels increased in both sublines reaching up to 200% of the concentrations prior to benzamide treatment. These results demonstrate an adaptative response of NAD⁺ metabolism to UV_254nm irradiation. In parallel, we observed a differential repartitioning of ADP-ribosyl residues between the NAD⁺ and poly(ADP-ribose) pools of LY-R and LY-S cells that correlates with the differential UV sensitivity of these cells.     

Characterization of a UV-resistant strain,UVr-10, established from a human clonal cell line,RSb, with high sensitivity to UV, 4NQO,MNNG and interferon

Characterization was performed of a UV-resistant variant strain, UV^r-10, derived from a human clonal cell line, RSb, with high sensitivity not only to the lethal effect of 254-nm far-ultraviolet (UV) irradiation but also to the effects of 4-nitroquinoline 1-oxide (4NQO) and N-methyl-N′-nitro-N-nitrosoguanidine (MNNG), and to the cell proliferation inhibition (CPI) effect of human leukocyte interferon (HuIFN-α) preparations.Colony-formation assays confirmed the increased resistance of UV^r-10 cells to both UV and 4NQO, but no increased resistance to MNNG. The marked recovery from the inhibition of the total cellular DNA synthesis of UV^r-10 cells, estimated by [methyl-³H]thymidine ([³H]dThd) uptake into the cellular DNA materials, was seen during 6 h after irradiation or 4NQO treatment even under the conditions without the recovery uptake into those of the parent RSb cells, but not during 6 h after MNNG treatment. Comparative studies on the activity of DNA repair synthesis between UV^r-10 and RSb cells, by measuring the extent of UV-, 4NQO- or MNNG-induced unscheduled DNA synthesis (UDS) and DNA repair replication, revealed an increased activity of UV^r-10 cells to UV and 4NQO but no significant increase of the activity to MNNG. These results suggest that increased DNA repair activities of a UV^r-10 cell line may account for its becoming resistant to the lethal effect of UV and 4NQO.Concerning the CPI effect of HuIFN-α, UV^r-10 cells showed increased resistance. Further, the DNA synthesis activity of UV^r-10 cells was not so inhibited by HuIFN-α exposure as that of RSb cells. However, HuIFN-α-exposed UV^r-10 cells showed more enhanced levels of activity of pppA(2′p5′A)_n synthetase (2–5A synthetase) than the exposed RSb, thus suggesting that HuIFN-α could exert enough intracellular effect even in UV^r-10 cells.The implication of the increased resistance of UV^r-10 cells to the effects of UV, 4NQO and HuIFN-α, but not to those of MNNG, is discussed.     

Identification of vitamin A-free cells in a stellate cell-enriched fraction of normal rat liver as myofibroblasts

Myofibroblasts (MFs) as well as hepatic stellate cells (HSCs) are known to be involved in liver fibrogenesis. Quiescent HSCs (qHSCs) in culture have been thought to differentiate to replicative activated HSCs (aHSCs). In this study a qHSC-enriched fraction isolated by Nycodenz-isodensity centrifugation was separated with a fluorescence-activated cell sorter, which revealed the presence of a small fraction (occupancy rate = 0.4%) of cells that did not show vitamin A-autofluorescence under ultraviolet (UV)-irradiation (UV⁻ cells). The remaining vitamin A-containing cells were autofluorescent (UV⁺) and originally expressed markers of qHSCs, and, in culture, did not grow, lost vitamin A, and expressed markers of aHSCs. UV⁻ cells showed morphology of MFs, and, in culture, grew to form colonies and expressed markers of MFs. These results indicated that UV⁺ and UV⁻ cells represent qHSCs and MFs, respectively, and that aHSCs have no growth potential and are a cell-type distinct from proliferative MFs. Gene expression profiles of UV⁻ cells (MFs) newly identified gremlin as one of MF-preferential genes and its proteins were localized around fibrotic septa in rat and human livers. In addition, we suggested that the qHSC-enriched fraction included approximately 6% of liver MFs.