A new structural insight into XPA–DNA interactions

XPA (xeroderma pigmentosum group A) protein is an essential factor for NER (nucleotide excision repair) which is believed to be involved in DNA damage recognition/verification, NER factor recruiting and stabilization of repair intermediates. Past studies on the structure of XPA have focused primarily on XPA interaction with damaged DNA. However, how XPA interacts with other DNA structures remains unknown though recent evidence suggest that these structures could be important for its roles in both NER and non-NER activities. Previously, we reported that XPA recognizes undamaged DNA ds/ssDNA (double-strand/single-strandDNA) junctions with a binding affinity much higher than its ability to bind bulky DNA damage. To understand how this interaction occurs biochemically we implemented a structural determination of the interaction using a MS-based protein footprinting method and limited proteolysis. By monitoring surface accessibility of XPA lysines to NHS-biotin modification in the free protein and the DNA junction-bound complex we show that XPA physically interacts with the DNA junctions via two lysines, K168 and K179, located in the previously known XPA(98–219) DBD (DNA-binding domain). Importantly, we also uncovered new lysine residues, outside of the known DBD, involved in the binding. We found that residues K221, K222, K224 and K236 in the C-terminal domain are involved in DNA binding. Limited proteolysis analysis of XPA–DNA interactions further confirmed this observation. Structural modelling with these data suggests a clamp-like DBD for the XPA binding to ds/ssDNA junctions. Our results provide a novel structure-function view of XPA–DNA junction interactions.     

Temporal and spatial distribution of ammonia-oxidizing organisms of two types of wetlands in Northeast China

Applied Microbiology and Biotechnology - Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) contribute significantly to the nitrogen cycle. The community structure of AOA and AOB...     

Beauty Matters: Social Preferences in a Three-Person Ultimatum Game

Preference for beauty is human nature, as previous behavior studies have supported the notion of “beauty premium” in which attractive people were more easily to get promoted and receive higher salaries. In the present study, 29 males were recruited to participate in a three-person ultimatum game (UG) including a proposer, a responder and a powerless third player. Each subject, playing as the responder, had to decide whether to accept an offer from the allocator both for himself and a female third person. We aimed to elucidate how the facial attractiveness of the female subject affected the male subjects’ fairness and decision-making in social exchanges. Frontal feedback-related negativity (FRN) in response to four offers in an attractive-face condition revealed no significant differences between offers; however, when the companion was an unattractive female, an “unfair/fair” offer, which assigned a lower share to the responder and a fair share to the third player, elicited the largest FRN. Furthermore, when the third player was offered the smallest amount (“fair/unfair” offer), a larger FRN was generated in an attractive-face condition than unattractive-face condition. In the “unfair/fair” offer condition in which subjects received a smaller allocation than the third person, the beauty of their female counterparts attenuated subjects’ aversion to inequality, resulting in a less negative FRN in the frontal region and an increased acceptance ratio. However, the influence of the third player’s facial attractiveness only affected the early evaluation stage: late P300 was found to be immune to the “beauty premium”. Under the two face conditions, P300 was smallest following an “unfair/fair” offer, whereas the amplitudes in the other three offer conditions exhibited no significant differences. In addition, the differentiated neural features of processing facial attractiveness were also determined and indexed by four event-related potentials (ERP) components: N170, frontal N1, N2 and late positive potentials (LPPs).     

Multiple mechanisms contributed to the reduced stability of Inner Mongolia grassland ecosystem following nitrogen enrichment

Plant and Soil - Global nitrogen enrichment has been identified as a major environmental problem that poses a threat to ecosystem functioning. However, there is no consensus on the impact of...     

Cholesterol modulates function of connexin 43 gap junction channel via PKC pathway in H9c2 cells

It has been shown that cholesterol modulates activity of protein kinase C (PKC), and PKC phosphorylates connexin 43 (Cx43) to regulate its function, respectively. However, it is not known whether cholesterol modulates function of Cx43 through regulating activity of PKC. In the present study, we demonstrated that cholesterol enrichment reduced the dye transfer ability of Cx43 in cultured H9c2 cells. Western blot analysis indicated that cholesterol enrichment enhanced the phosphorylated state of Cx43. Immunofluorescent images showed that cholesterol enrichment made the Cx43 distribution from condensed to diffused manner in the interface between the cells. In cholesterol enriched cells, PKC antagonists partially restored the dye transfer ability among the cells, downregulated the phosphorylation of Cx43 and redistributed Cx43 from the diffused manner to the condensed manner in the cell interface. In addition, reduction of cholesterol level suppressed PKC activity to phosphorylate Cx43 and restored Cx43 function in PKC agonist-treated cells. Furthermore, we demonstrated that cholesterol enrichment upregulated the phosphorylated state of Cx43 at Ser368, while PKC antagonists reversed the effect. Taken together, cholesterol level in the cells plays important roles in regulating Cx43 function through activation of the PKC signaling pathway.     

All members in the sphingomyelin synthase gene family have ceramide phosphoethanolamine synthase activity

Sphingomyelin synthase-related protein (SMSr) synthesizes the sphingomyelin analog ceramide phosphoethanolamine (CPE) in cells. Previous cell studies indicated that SMSr is involved in ceramide homeostasis and is crucial for cell function. To further examine SMSr function in vivo, we generated Smsr KO mice that were fertile and had no obvious phenotypic alterations. Quantitative MS analyses of plasma, liver, and macrophages from the KO mice revealed only marginal changes in CPE and ceramide as well as other sphingolipid levels. Because SMS2 also has CPE synthase activity, we prepared Smsr/Sms2 double KO mice. We found that CPE levels were not significantly changed in macrophages, suggesting that CPE levels are not exclusively dependent on SMSr and SMS2 activities. We then measured CPE levels in Sms1 KO mice and found that Sms1 deficiency also reduced plasma CPE levels. Importantly, we found that expression of Sms1 or Sms2 in SF9 insect cells significantly increased not only SM but also CPE formation, indicating that SMS1 also has CPE synthase activity. Moreover, we measured CPE synthase K_m and V_max for SMS1, SMS2, and SMSr using different NBD ceramides. Our study reveals that all mouse SMS family members (SMSr, SMS1, and SMS2) have CPE synthase activity. However, neither CPE nor SMSr appears to be a critical regulator of ceramide levels in vivo.     

Inorganic and Organic Nitrogen Acquisition by a Fern Dicranopteris dichotoma in a Subtropical Forest in South China

The fern Dicranopteris dichotoma is an important pioneer species of the understory in Masson pine (Pinus massoniana) forests growing on acidic soils in the subtropical and tropical China. To improve our understanding of the role of D. dichotoma in nitrogen (N) uptake of these forests, a short-term ¹⁵N experiment was conducted at mountain ridge (MR, with low N level) and mountain foot (MF, with high N level). We injected ¹⁵N tracers as ¹⁵NH₄, ¹⁵NO₃ or ¹⁵N-glycine into the soil surrounding each plant at both MR and MF sites. Three hours after tracer injection, the fern D. dichotoma took up ¹⁵NH₄ ⁺ significantly faster at MF than at MR, but it showed significantly slower uptake of ¹⁵NO₃ ⁻ at MF than at MR. Consequently, ¹⁵NO₃ ⁻ made greater contribution to the total N uptake (50% to the total N uptake) at MR than at MF, but ¹⁵N-glycine only contributed around 11% at both sites. Twenty-four hours after tracer injection, D. dichotoma preferred ¹⁵NH₄ ⁺ (63%) at MR, whereas it preferred ¹⁵NO₃ ⁻ (47%) at MF. We concluded that the D. dichotoma responds distinctly in its uptake pattern for three available N species over temporal and spatial scales, but mainly relies on inorganic N species in the subtropical forest. This suggests that the fern employs different strategies to acquire available N which depends on N levels and time.