Functional genomics of the yeast DNA-damage response

High-throughput approaches are beginning to have an impact on many areas of yeast biology. Two recent studies, using different experimental platforms, provide insight into new pathways involved in the response of yeast to DNA damage.     

TAK1 is critical for IkappaB kinase-mediated activation of the NF-kappaB pathway

Cytokine treatment stimulates the IkappaB kinases, IKKalpha and IKKbeta, which phosphorylate the IkappaB proteins, leading to their degradation and activation of NF-kappaB regulated genes. A clear definition of the specific roles of IKKalpha and IKKbeta in activating the NF-kappaB pathway and the upstream kinases that regulate IKK activity remain to be elucidated. Here, we utilized small interfering RNAs (siRNAs) directed against IKKalpha, IKKbeta and the upstream regulatory kinase TAK1 in order to better define their roles in cytokine-induced activation of the NF-kappaB pathway. In contrast to previous results with mouse embryo fibroblasts lacking either IKKalpha or IKKbeta, which indicated that only IKKbeta is involved in cytokine-induced NF-kappaB activation, we found that both IKKalpha and IKKbeta were important in activating the NF-kappaB pathway. Furthermore, we found that the MAP3K TAK1, which has been implicated in IL-1-induced activation of the NF-kappaB pathway, was also critical for TNFalpha-induced activation of the NF-kappaB pathway. TNFalpha activation of the NF-kappaB pathway is associated with the inducible binding of TAK1 to TRAF2 and both IKKalpha and IKKbeta. This analysis further defines the distinct in vivo roles of IKKalpha, IKKbeta and TAK1 in cytokine-induced activation of the NF-kappaB pathway.     

Effect of resource competition on the long-term allocation of grooming by female baboons: evaluating Seyfarth's model

Seyfarth (1977, Journal of Theoretical Biology, 65, 671-698) proposed an influential model that explained the long-term patterning of grooming relationships between female primates in terms of an interaction between the idealized grooming objectives of females and competition for valuable grooming partners. A critical test of the model requires a demonstration not only that competition for partners exists, but also that females do have an underlying target for the amount of grooming that they would like to receive relative to the amount they need to give. As it is not possible to stipulate a priori what this target is, or to detect it directly, we assessed its applicability by making a set of predictions, within the framework of Seyfarth's model, as to how observed grooming patterns should change with changes in the intensity of resource competition. We tested these predictions with data from a troop of baboons, Papio hamadryas ursinus, for which the within-bout structure of grooming has already been shown to be sensitive to changes in resource competition (Barrett et al. 2002, Animal Behaviour, 63, 1047-1053). We found no evidence of competition for grooming partners and our results do not support the predictions of the modified model with respect to the existence of underlying grooming objectives. The findings that the grooming of female baboons is more diverse and that the mean rank distance separating partners increases when resource competition is greater, together with the absence of rank effects on long-term patterns, are, however, supportive of the recent biological market approach to social interactions. Copyright 2003 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved.      

DNA-Dependent Protein Kinase Phosphorylation of IκBα and IκBβ Regulates NF-κB DNA Binding Properties

Regulation of the IκBα and IκBβ proteins is critical for modulating NF-κB-directed gene expression. Both IκBα and IκBβ are substrates for cellular kinases that phosphorylate the amino and carboxy termini of these proteins and regulate their function. In this study, we utilized a biochemical fractionation scheme to purify a kinase activity which phosphorylates residues in the amino and carboxy termini of both IκBα and IκBβ. Peptide microsequence analysis by capillary high-performance liquid chromatography ion trap mass spectroscopy revealed that this kinase was the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). DNA-PK phosphorylates serine residue 36 but not serine residue 32 in the amino terminus of IκBα and also phosphorylates threonine residue 273 in the carboxy terminus of this protein. To determine the biological relevance of DNA-PK phosphorylation of IκBα, murine severe combined immunodeficiency (SCID) cell lines which lack the DNA-PKcs gene were analyzed. Gel retardation analysis using extract prepared from these cells demonstrated constitutive nuclear NF-κB DNA binding activity, which was not detected in extracts prepared from SCID cells complemented with the human DNA-PKcs gene. Furthermore, IκBα that was phosphorylated by DNA-PK was a more potent inhibitor of NF-κB binding than nonphosphorylated IκBα. These results suggest that DNA-PK phosphorylation of IκBα increases its interaction with NF-κB to reduce NF-κB DNA binding properties.     

Reproduction and survival of suricates (Suricata suricatta) in the southern Kalahari

In most respects, the demography of Kalahari suricates (Suricata suricatta) resembles that of other social mongooses. Average group size varies from four to nine, and groups typically include several mature females, of which one is responsible for the majority of breeding attempts. Breeding females show a postpartum oestrus; gestation is around 60 days; litter size is three to five pups at emergence and females rarely breed before the age of 24 months. In contrast, annual survival rates (0.20 for pups and 0.43 for animals over one year old) are lower than those recorded in other species. Breeding frequency is related to rainfall and breeding can cease altogether when rainfall is unusually low. In a year when this occurred, group size eroded rapidly and over 60% of groups became extinct. Total numbers were slow to recover during the following year because emigration by females was infrequent and new groups did not form in vacant ranges created by the extinction of groups. High rates of group extinction have been found in other cooperative breeders and may occur because breeding success and survival show inverse density dependence.     

Predation, group size and mortality in a cooperative mongoose, Suricata suricatta

1. In social mammals where group members cooperate to detect predators and raise young, members of small groups commonly show higher mortality or lower breeding success than members of large ones. It is generally assumed that this is because large group size allows individuals to detect or repel predators more effectively but other benefits of group size may also be involved, including reduced costs of raising young and more effective competition for resources with neighbouring groups.
2. To investigate the extent to which predation rate affects survival, we compared mortality rates in two populations of suricates ( Suricata suricatta ), one living in an area of high predator density (Kalahari Gemsbok Park) and one living in an area of relatively low predator density (neighbouring ranchland). Most aspects of feeding ecology and growth (including time spent feeding, daily weight gain, growth, adult body weight, breeding frequency and neonatal mortality) were similar in the two populations. In contrast, mortality of animals over 3 months old was 1·7 times higher in the Park than on ranchland.
3. Mortality of juveniles between emergence from the natal burrow and 6 months of age was higher in small groups than large ones in the Park but significantly lower in small groups than large ones on ranchland. Adult mortality declined in larger groups in both areas.
4. The tendency for survival to be low in small groups had far-reaching consequences for the risk of group extinction. During a year of low rainfall in the Park, all groups of less than nine animals became extinct and population density declined to around a third of its initial level. We argue that high group extinction rates are to be expected in species where survival declines in small groups and mortality rates are high.