A structural approach reveals how neighbouring C2H2 zinc fingers influence DNA binding specificity

Development of an accurate protein–DNA recognition code that can predict DNA specificity from protein sequence is a central problem in biology. C₂H₂ zinc fingers constitute by far the largest family of DNA binding domains and their binding specificity has been studied intensively. However, despite decades of research, accurate prediction of DNA specificity remains elusive. A major obstacle is thought to be the inability of current methods to account for the influence of neighbouring domains. Here we show that this problem can be addressed using a structural approach: we build structural models for all C₂H₂-ZF–DNA complexes with known binding motifs and find six distinct binding modes. Each mode changes the orientation of specificity residues with respect to the DNA, thereby modulating base preference. Most importantly, the structural analysis shows that residues at the domain interface strongly and predictably influence the binding mode, and hence specificity. Accounting for predicted binding mode significantly improves prediction accuracy of predicted motifs. This new insight into the fundamental behaviour of C₂H₂-ZFs has implications for both improving the prediction of natural zinc finger-binding sites, and for prioritizing further experiments to complete the code. It also provides a new design feature for zinc finger engineering.     

Activation of PKR causes amyloid ß-peptide accumulation via de-repression of BACE1 expression

BACE1 is a key enzyme involved in the production of amyloid ß-peptide (Aß) in Alzheimer''s disease (AD) brains. Normally, its expression is constitutively inhibited due to the presence of the 5′untranslated region (5′UTR) in the BACE1 promoter. BACE1 expression is activated by phosphorylation of the eukaryotic initiation factor (eIF)2-alpha, which reverses the inhibitory effect exerted by BACE1 5′UTR. There are four kinases associated with different types of stress that could phosphorylate eIF2-alpha. Here we focus on the double-stranded (ds) RNA-activated protein kinase (PKR). PKR is activated during viral infection, including that of herpes simplex virus type 1 (HSV1), a virus suggested to be implicated in the development of AD, acting when present in brains of carriers of the type 4 allele of the apolipoprotein E gene. HSV1 is a dsDNA virus but it has genes on both strands of the genome, and from these genes complementary RNA molecules are transcribed. These could activate BACE1 expression by the PKR pathway. Here we demonstrate in HSV1-infected neuroblastoma cells, and in peripheral nervous tissue from HSV1-infected mice, that HSV1 activates PKR. Cloning BACE1 5′UTR upstream of a luciferase (luc) gene confirmed its inhibitory effect, which can be prevented by salubrinal, an inhibitor of the eIF2-alpha phosphatase PP1c. Treatment with the dsRNA analog poly (I∶C) mimicked the stimulatory effect exerted by salubrinal over BACE1 translation in the 5′UTR-luc construct and increased Aß production in HEK-APPsw cells. Summarizing, our data suggest that PKR activated in brain by HSV1 could play an important role in the development of AD.     

Biogeochemistry of Mariana Islands coastal sediments: terrestrial influence on /gd13, Ash,CaCO3, Al,Fe, Si and P

Stable C isotope ratios (¹³C-PDB), percentages of organic matter, and HCl insoluble ash and soluble carbonates, extractable Fe, Al, Si and P were used to determine the distribution and accumulation of terrestrial material in reef-flat moats and lagoons of two high islands (Guam and Saipan) in the western tropical Pacific. Carbonate sediments of a reef-flat moat infiltrated by seepage of aquifer waters (but without surface runoff) were depleted in both P (by 38%) and ¹³C (by 41%) and enriched in Si (by 100%) relative to offshore lagoon sediments. Iron and ash accumulated in depositional regimes regardless of the occurrence of runoff but was depleted from coarse-grained carbonates in turbulent regimes. Aluminum (>ca. 10 to 20 mol g^-1), Fe (>ca. 1 to 3 mol g^-1) and ash (>0.5%) indicated terrigenous influence which was corroborated by depletions in both ¹³C and P. Low-salinity geochemical segregation, natural biochemical accumulation, as well as long-shore currents and eddies help sequester these materials nearshore.     

N-glycans on Nipah virus fusion protein protect against neutralization but reduce membrane fusion and viral entry

Nipah virus (NiV) is a deadly emerging paramyxovirus. The NiV attachment (NiV-G) and fusion (NiV-F) envelope glycoproteins mediate both syncytium formation and viral entry. Specific N-glycans on paramyxovirus fusion proteins are generally required for proper conformational integrity and biological function. However, removal of individual N-glycans on NiV-F had little negative effect on processing or fusogenicity and has even resulted in slightly increased fusogenicity. Here, we report that in both syncytium formation and viral entry assays, removal of multiple N-glycans on NiV-F resulted in marked increases in fusogenicity (>5-fold) but also resulted in increased sensitivity to neutralization by NiV-F-specific antisera. The mechanism underlying the hyperfusogenicity of these NiV-F N-glycan mutants is likely due to more-robust six-helix bundle formation, as these mutants showed increased fusion kinetics and were more resistant to neutralization by a fusion-inhibitory reagent based on the C-terminal heptad repeat region of NiV-F. Finally, we demonstrate that the fusogenicities of the NiV-F N-glycan mutants were inversely correlated with the relative avidities of NiV-F's interactions with NiV-G, providing support for the attachment protein "displacement" model of paramyxovirus fusion. Our results indicate that N-glycans on NiV-F protect NiV from antibody neutralization, suggest that this "shielding" role comes together with limiting cell-cell fusion and viral entry efficiencies, and point to the mechanisms underlying the hyperfusogenicity of these N-glycan mutants. These features underscore the varied roles that N-glycans on NiV-F play in the pathobiology of NiV entry but also shed light on the general mechanisms of paramyxovirus fusion with host cells.     

Expression of the p12 subunit of human DNA polymerase δ (Pol δ), CDK inhibitor p21WAF1, Cdt1, cyclin A,PCNA and Ki-67 in relation to DNA replication in individual cells

We recently reported that the p12 subunit of human DNA polymerase δ (Pol δ4) is degraded by CRL4^Cdt2 which regulates the licensing factor Cdt1 and p21^WAF1 during the G₁ to S transition. Presently, we performed multiparameter laser scanning cytometric analyses of changes in levels of p12, Cdt1 and p21^WAF1, detected immunocytochemically in individual cells, vis-à-vis the initiation and completion of DNA replication. The latter was assessed by pulse-labeling A549 cells with the DNA precursor ethynyl-2′-deoxyribose (EdU). The loss of p12 preceded the initiation of DNA replication and essentially all cells incorporating EdU were p12 negative. Completion of DNA replication and transition to G₂ phase coincided with the re-appearance and rapid rise of p12 levels. Similar to p12 a decline of p21^WAF1 and Cdt1 was seen at the end of G₁ phase and all DNA replicating cells were p21^WAF1 and Cdt1 negative. The loss of p21^WAF1 preceded that of Cdt1 and p12 and the disappearance of the latter coincided with the onset of DNA replication. Loss of p12 leads to conversion of Pol δ4 to its trimeric form, Pol δ3, so that the results provide strong support to the notion that Pol δ3 is engaged in DNA replication during unperturbed progression through the S phase of cell cycle. Also assessed was a correlation between EdU incorporation, likely reflecting the rate of DNA replication in individual cells, and the level of expression of positive biomarkers of replication cyclin A, PCNA and Ki-67 in these cells. Of interest was the observation of stronger correlation between EdU incorporation and expression of PCNA (r = 0.73) than expression of cyclin A (r = 0.47) or Ki-67 (r = 0.47).     

Partitioning seasonal time: interactions among size, foraging activity and diet in leaf-litter frogs

This study investigates hypotheses about partitioning of food resources among all species and several size classes in an assemblage of diurnal leaf-litter frogs in central Amazonia. All species in this assemblage change the type and size of prey as they grow. An ordination of diet composition was significantly associated with frog size and species-specific behaviour. However, a partial Mantel analysis indicated that species explained about 1.5 times more of the variation in diet overlap between individuals than frog size. Diet and foraging activity are correlated in juveniles, but not in adults, and this result holds whether species are considered as statistically independent observations or whether relationships are analysed using phylogenetically independent contrasts. This study showed that the partitioning of food resources between species changes with the population size structures. Thus, intraspecific and interspecific changes in diet, coupled with different patterns of juvenile recruitment, cause diet segregation among species due to temporal segregation of equivalent size classes. Received: 25 August 1997 / Accepted: 1 April 1998     

Cardioprotection involves activation of NF-kappa B via PKC-dependent tyrosine and serine phosphorylation of I kappa B-alpha

Previous studies indicated that activation of PKC and Src tyrosine kinases by ischemic preconditioning (PC) may participate in the activation of NF-kappa B. However, the molecular mechanisms underlying activation of NF-kappa B during ischemic PC remain unknown. In the hearts of conscious rabbits, it was found that ischemic PC (6 cycles of 4-min coronary occlusion and 4-min reperfusion) significantly induced both tyrosine (+226.9 +/- 42%) and serine (+137.0 +/- 36%) phosphorylation of the NF-kappa B inhibitory protein I kappa B-alpha, concomitant with increased activation of the I kappa B-alpha kinases IKK alpha (+255.0 +/- 46%) and IKK beta (+173.1 +/- 35%). Furthermore, both tyrosine and serine phosphorylation of I kappa B-alpha were blocked by pretreatment with either the nonreceptor tyrosine kinase inhibitor lavendustin-A (LD-A) or the PKC inhibitor chelerythrine (Che) (both given at doses previously shown to block ischemic PC). Interestingly, Che completely abolished PC-induced activation of IKK alpha/beta, whereas LD-A had no effect. In addition, I kappa B-alpha protein level did not change during ischemic PC. Together, these data indicate that ischemic PC-induced activation of NF-kappa B occurs through both tyrosine and serine phosphorylation of I kappa B-alpha and is regulated by nonreceptor tyrosine kinases and PKC.     

A potent mechanism-inspired O-GlcNAcase inhibitor that blocks phosphorylation of tau in vivo

Pathological hyperphosphorylation of the microtubule-associated protein tau is characteristic of Alzheimer's disease (AD) and the associated tauopathies. The reciprocal relationship between phosphorylation and O-GlcNAc modification of tau and reductions in O-GlcNAc levels on tau in AD brain offers motivation for the generation of potent and selective inhibitors that can effectively enhance O-GlcNAc in vertebrate brain. We describe the rational design and synthesis of such an inhibitor (thiamet-G, K(i) = 21 nM; 1) of human O-GlcNAcase. Thiamet-G decreased phosphorylation of tau in PC-12 cells at pathologically relevant sites including Thr231 and Ser396. Thiamet-G also efficiently reduced phosphorylation of tau at Thr231, Ser396 and Ser422 in both rat cortex and hippocampus, which reveals the rapid and dynamic relationship between O-GlcNAc and phosphorylation of tau in vivo. We anticipate that thiamet-G will find wide use in probing the functional role of O-GlcNAc in vertebrate brain, and it may also offer a route to blocking pathological hyperphosphorylation of tau in AD.     

MITOTIC ACTIVITY AT THE SHOOT APEX OF AZOLLA FILICULOIDES

The mosquito fern, Azolla filiculoides Lam., was grown in a growth chamber on a nitrogen-free culture solution at 24 C under the following photoperiod: 16 hr light/8 hr darkness. Shoot tips were fixed every 2 hr for 24 hr to determine the mitotic index for the apical cell, immediate derivatives, and remaining cells to the level of the first leaf or lateral shoot primordium. Mitotic indices were 6.9%, 6.5% and 6.3%, respectively. The colchicine method was employed to determine the cell-cycle durations and duration of mitosis for the same populations of cells. The cell-cycle duration and duration of mitosis of the apical cell were 28.2 hr and 2.8 hr, respectively; for the immediate derivatives, 26.7 hr and 2.5 hr; for the remaining cells, 23.6 hr and 2.1 hr. Conclusions: the apical cell is as mitotically active as its immediate derivatives, and there is no evidence of a quiescent apical cell.