Toward a PKB inhibitor: modification of a selective PKA inhibitor by rational design

Protein kinase B/Akt (PKB) is an anti-apoptotic protein kinase that has strongly elevated activity in human malignancies. We therefore initiated a program to develop PKB inhibitors, "Aktstatins". We screened about 500 compounds for PKB inhibitors, using a radioactive assay and an ELISA assay that we established for this purpose. These compounds were produced as combinatorial libraries, designed using the structure of the selective PKA inhibitor H-89 as a starting point. We have identified a successful lead compound, which inhibits PKB activity in vitro and in cells overexpressing active PKB. The new compound shows reversed selectivity to H-89: In contrast to H-89, which inhibits PKA 70 times better than PKB, the new compound, NL-71-101, inhibits PKB 2.4-fold better than PKA. The new compound, but not H-89, induces apoptosis in tumor cells in which PKB is amplified. We have identified structural features in NL-71-101 that are significant for the specificity and that can be used for future development and optimization of PKB inhibitors.     

How to move with no rigid skeleton? The octopus has the answers

The octopus is amazingly flexible and shows exceptional control and coordination in all its movements. It seems remarkable to us skeletal creatures that the octopus achieves all this without a single bone.     

The Middle Subunit of Replication Protein A Contacts Growing RNA-DNA Primers in Replicating Simian Virus 40 Chromosomes

The eukaryotic single-stranded DNA binding protein replication protein A (RPA) participates in major DNA transactions. RPA also interacts through its middle subunit (Rpa2) with regulators of the cell division cycle and of the response to DNA damage. A specific contact between Rpa2 and nascent simian virus 40 DNA was revealed by in situ UV cross-linking. The dynamic attributes of the cross-linked DNA, namely, its size distribution, RNA primer content, and replication fork polarity, were determined. These data suggest that Rpa2 contacts the early DNA chain intermediates synthesized by DNA polymerase α-primase (RNA-DNA primers) but not more advanced products. Possible signaling functions of Rpa2 are discussed, and current models of eukaryotic lagging-strand DNA synthesis are evaluated in view of our results.     

Present–absent: a chronicle of the dinoflagellate Peridinium gatunense from Lake Kinneret

A long-term record dating back to the 1960s indicates that Peridinium gatunense, an armored dinoflagellate, dominated the phytoplankton of Lake Kinneret (Sea of Galilee, Israel) until the mid-1990s, with a relatively stable spring bloom. However, since 1996, these blooms became irregular, failing to develop in 10 out of the past 16 years. During the later period, a significant correlation (R ² = 0.605, P = 0.013) was found between annual peak P. gatunense biomass and riverine inflow volume. In-lake surveys showed that patches of high P. gatunense densities were associated with water enriched with fresher inflowing Jordan River water. Supplementing laboratory cultures of P. gatunense with Hula Valley water stimulated its growth relative to un-enriched controls. A likely explanation to the recent irregular blooms of this dinoflagellate is a hydrological modification that was made in the catchment in the mid-1990s, preventing Hula Valley water from reaching Lake Kinneret in most years—except for exceptionally wet years. We propose that until the mid-1990s, the Jordan River water enriched Lake Kinneret with a growth factor (a microelement and/or organic compound) originating in the Hula Valley, which in recent years has arrived in sufficient quantities to support a bloom only in high-rainfall years.     

Leishmania express a functional Cdc20 homologue

Our knowledge concerning the mechanisms of cell cycle regulation in organisms belonging to the Trypanosometidae family is limited. Leishmania donovani are parasitic protozoa that cause kala azar, a fatal form of visceral leishmaniasis in humans. Here we provide evidence that the L. donovani genome contains a Cdc20 homologue. Cdc20 is a regulator of the Anaphase Promoting Complex/Cyclosome (APC/C) that mediates ubiquitin-dependent proteasomal degradation of key cell cycle regulators in eukaryotes. We show that L. donovani Cdc20 protein (LdCdc20p) can complement a lack of yeast Cdc20 protein in Saccharomyces cerevisiae cells, validating the functionality of LdCdc20p. Furthermore, we demonstrate cyclic expression of LdCdc20p and that it contains an active RXXL destruction motif, a distinctive feature of proteins targeted for proteasomal degradation by APC/C. Finally, in line with the proteasome mediating LdCdc20p degradation, promastigotes exposed to proteasome inhibitor display elevated LdCdc20p levels. Taken together our data indicate that Leishmania regulate their cell cycle by ubiquitin-dependent proteasomal degradation mediated by the APC/C.     

Evolutionary constraints on polyembryony in parasitic wasps: a simulation model

Polyembryony involves the production of several genetically identical progeny from a single egg through clonal division. Although polyembryonic development allows highly efficient reproduction, especially in some parasitoid wasps, it is far less common than monoembryony (development of one embryo per egg). To understand what might constrain the evolutionary success of polyembryony in parasitoids, we developed Monte Carlo models that simulate the competition between polyembryonic females and their monoembryonic counterparts. We investigated which simulated life‐history traits of the females allow the monoembryonic mode of development to succeed. Published empirical studies were surveyed to explore whether these traits indeed differ between polyembryonic parasitoids and related monoembryonic species. The simulations predict an advantage to monoembryony in parasitoids whose reproduction is limited by host availability rather than by egg supply, and that parasitize small‐bodied hosts. Comparative data on the parasitoid families Encyrtidae and (to a lesser extent) Braconidae, but not the data from Platygastridae, circumstantially support these predictions. The model also predicts monoembryony to outcompete polyembryony when: 1) hosts vary considerably in quality, 2) polyembryonic development carries high physiological costs, and 3) monoembryonic females make optimal clutch size decisions upon attacking hosts. These multiple constraints may account for the rarity of polyembryony among parasitoid species.     

Involvement of Toll-like receptor 4 in acetaminophen hepatotoxicity

The objective of this study was to determine whether Toll-like receptor 4 (TLR4) has a role in alcohol-mediated acetaminophen (APAP) hepatotoxicity. TLR4 is involved in the inflammatory response to endotoxin. Others have found that ethanol-mediated liver disease is decreased in C3H/HeJ mice, which have a mutated TLR4 resulting in a decreased response to endotoxin compared with endotoxin-responsive mice. In the present study, short-term (1 wk) pretreatment with ethanol plus isopentanol, the predominant alcohols in alcoholic beverages, caused no histologically observed liver damage in either C3H/HeJ mice or endotoxin-responsive C3H/HeN mice, despite an increase in nitrotyrosine levels in the livers of C3H/HeN mice. In C3H/HeN mice pretreated with the alcohols, subsequent exposure to APAP caused a transient decrease in liver nitrotyrosine formation, possibly due to competitive interaction of peroxynitrite with APAP producing 3-nitroacetaminophen. Treatment with APAP alone resulted in steatosis in addition to congestion and necrosis in both C3H/HeN and C3H/HeJ mice, but the effects were more severe in endotoxin-responsive C3H/HeN mice. In alcohol-pretreated endotoxin-responsive C3H/HeN mice, subsequent exposure to APAP resulted in further increases in liver damage, including severe steatosis, associated with elevated plasma levels of TNF-alpha. In contrast, alcohol pretreatment of C3H/HeJ mice caused little to no increase in APAP hepatotoxicity and no increase in plasma TNF-alpha. Portal blood endotoxin levels were very low and were not detectably elevated by any of the treatments. In conclusion, this study implicates a role of TLR4 in APAP-mediated hepatotoxicity.     

Analysis of mercuric reductase (merA) gene diversity in an anaerobic mercury-contaminated sediment enrichment

The reduction of ionic mercury to elemental mercury by the mercuric reductase (MerA) enzyme plays an important role in the biogeochemical cycling of mercury in contaminated environments by partitioning mercury to the atmosphere. This activity, common in aerobic environments, has rarely been examined in anoxic sediments where production of highly toxic methylmercury occurs. Novel degenerate PCR primers were developed which span the known diversity of merA genes in Gram-negative bacteria and amplify a 285 bp fragment at the 3' end of merA. These primers were used to create a clone library and to analyse merA diversity in an anaerobic sediment enrichment collected from a mercury-contaminated site in the Meadowlands, New Jersey. A total of 174 sequences were analysed, representing 71 merA phylotypes and four novel MerA clades. This first examination of merA diversity in anoxic environments suggests an untapped resource for novel merA sequences.     

Core promoter binding by histone-like TAF complexes

A major function of TFIID is core promoter recognition. TFIID consists of TATA-binding protein (TBP) and 14 TBP-associated factors (TAFs). Most of them contain a histone fold domain (HFD) that lacks the DNA-contacting residues of histones. Whether and how TAF HFDs contribute to core promoter DNA binding are yet unresolved. Here we examined the DNA binding activity of TAF9, TAF6, TAF4b, and TAF12, which are related to histones H3, H4, H2A, and H2B, respectively. Each of these TAFs has intrinsic DNA binding activity adjacent to or within the HFD. The DNA binding domains were mapped to evolutionarily conserved and essential regions. Remarkably, HFD-mediated interaction enhanced the DNA binding activity of each of the TAF6-TAF9 and TAF4b-TAF12 pairs and of a histone-like octamer complex composed of the four TAFs. Furthermore, HFD-mediated interaction stimulated sequence-specific binding by TAF6 and TAF9. These results suggest that TAF HFDs merge with other conserved domains for efficient and specific core promoter binding.