Progress of structural genomics initiatives: an analysis of solved target structures

The explosion in gene sequence data and technological breakthroughs in protein structure determination inspired the launch of structural genomics (SG) initiatives. An often stated goal of structural genomics is the high-throughput structural characterisation of all protein sequence families, with the long-term hope of significantly impacting on the life sciences, biotechnology and drug discovery. Here, we present a comprehensive analysis of solved SG targets to assess progress of these initiatives. Eleven consortia have contributed 316 non-redundant entries and 323 protein chains to the Protein Data Bank (PDB), and 459 and 393 domains to the CATH and SCOP structure classifications, respectively. The quality and size of these proteins are comparable to those solved in traditional structural biology and, despite huge scope for duplicated efforts, only 14% of targets have a close homologue (>/=30% sequence identity) solved by another consortium. Analysis of CATH and SCOP revealed the significant contribution that structural genomics is making to the coverage of superfamilies and folds. A total of 67% of SG domains in CATH are unique, lacking an already characterised close homologue in the PDB, whereas only 21% of non-SG domains are unique. For 29% of domains, structure determination revealed a remote evolutionary relationship not apparent from sequence, and 19% and 11% contributed new superfamilies and folds. The secondary structure class, fold and superfamily distributions of this dataset reflect those of the genomes. The domains fall into 172 different folds and 259 superfamilies in CATH but the distribution is highly skewed. The most populous of these are those that recur most frequently in the genomes. Whilst 11% of superfamilies are bacteria-specific, most are common to all three superkingdoms of life and together the 316 PDB entries have provided new and reliable homology models for 9287 non-redundant gene sequences in 206 completely sequenced genomes. From the perspective of this analysis, it appears that structural genomics is on track to be a success, and it is hoped that this work will inform future directions of the field.     

Identification of two distinct human immunodeficiency virus type 1 Vif determinants critical for interactions with human APOBEC3G and APOBEC3F

Human cytidine deaminases APOBEC3G (A3G) and APOBEC3F (A3F) inhibit replication of Vif-deficient human immunodeficiency virus type 1 (HIV-1). HIV-1 Vif overcomes these host restriction factors by binding to them and inducing their proteasomal degradation. The Vif-A3G and Vif-A3F interactions are attractive targets for antiviral drug development because inhibiting the interactions could allow the host defense mechanism to control HIV-1 replication. It was recently reported that the Vif amino acids D(14)RMR(17) are important for functional interaction and degradation of the previously identified Vif-resistant mutant of A3G (D128K-A3G). However, the Vif determinants important for functional interaction with A3G and A3F have not been fully characterized. To identify these determinants, we performed an extensive mutational analysis of HIV-1 Vif. Our analysis revealed two distinct Vif determinants, amino acids Y(40)RHHY(44) and D(14)RMR(17), which are essential for binding to A3G and A3F, respectively. Interestingly, mutation of the A3G-binding region increased Vif's ability to suppress A3F. Vif binding to D128K-A3G was also dependent on the Y(40)RHHY(44) region but not the D(14)RMR(17) region. Consistent with previous observations, subsequent neutralization of the D128K-A3G antiviral activity required substitution of Vif determinant D(14)RMR(17) with SEMQ, similar to the SERQ amino acids in simian immunodeficiency virus SIV(AGM) Vif, which is capable of neutralizing D128K-A3G. These studies are the first to clearly identify two distinct regions of Vif that are critical for independent interactions with A3G and A3F. Pharmacological interference with the Vif-A3G or Vif-A3F interactions could result in potent inhibition of HIV-1 replication by the APOBEC3 proteins.     

Fish communities on staghorn coral: effects of habitat characteristics and resident farmerfishes

Branching corals, like many in the genus Acropora, provide structurally complex habitats for reef fishes and other organisms. Fluctuations in the abundance, distribution and characteristics of thicket-forming staghorn Acroporids may contribute to changes in the abundance and species composition of reef fishes due to changes in the availability of shelter habitat and food. Farming damselfishes of the genus Stegastes can occur in high abundances in staghorn corals and actively defend food and nest space against organisms that threaten these resources. Here we assess the value of staghorn as habitat for fishes in the central South Pacific, and how the presence of territorial farming damselfishes may influence the assemblage of fishes that associate with staghorn corals. Surveys of 185 Acropora pulchra patches located in the lagoons surrounding the island of Moorea, French Polynesia revealed 85 species of fish from 25 families. Total fish abundance and species richness values ranged from no fish on a patch to a high of 275 individuals and 26 species. Patch area was the most important characteristic in explaining variation in attributes of the fish assemblage, with other characteristics explaining little of the species composition or trophic structure. Behavioral observations revealed that farming damselfishes were most aggressive toward corallivores, herbivores, and egg predators, while they ignored most carnivores and omnivores. Despite this pattern, we observed positive covariance between Stegastes and the group of fishes that elicited the strongest aggressive response when the effect of patch area was removed, suggesting these fishes remain drawn to the resources produced or enhanced by Stegastes on A. pulchra.     

The biology of Bracon celer as a parasitoid of the olive fruit fly

A series of laboratory experiments was conducted on a colony of Bracon celer Szépligeti (Hymenoptera: Braconidae) reared on the olive fly, Bactrocera oleae (Rossi) (Diptera: Tephritidae). Female B. celer preferentially probe and oviposit into olives containing late third-instar fly larvae. The parasitoid develops as a solitary, ectoparasitic idiobiont. Mean development time (oviposition to adult eclosion) at 22 °C was, for females, 36±1 (SE) days, and for males, 34±1 days. The mean longevity of adult female wasps when provided honey and water was significantly greater than when they were provided water alone, or nothing. The females produced an average of 9.7±7.2 progeny during their lifetimes, but production levels in the insectary colony suggested that this level of fecundity was artificially low and could be improved. The discrepancy may be a consequence of constraints on oviposition behavior imposed by the experimental design. The results are discussed with respect to insectary production methods and the potential use of B. celer as a biological control agent for olive fly in California.     

Effects of α2- and β-adrenoceptor agonists on growth hormone secretion following lesion of the noradrenergic system of the rat

The aim of the present investigation was to lesion the noradrenergic system and to measure the effect on growth hormone (GH) secretion following peripheral administration of ₂- and -adrenoceptor agonists. Direct injection of these agonists into the paraventricular nucleus of the hypothalamus (PVN) and its effect on GH secretion were also investigated. Systemic administration of N-2-chloroethyl-N-ethyl-2-bromobenzylamine (DSP₄, 60 mg/kg, injected i.p. 10 days prior to experimentation) significantly decreased the noradrenaline (NA) content of the hippocampus, frontal cortex and hypothalamus but had no effect on the dopamine (DA) or serotonin (5-HT) content of these areas. Bilateral injection of 6-hydroxydopamine (6-OHDA, 10 g/l, 14 days prior to experimentation) into the medial forebrain bundle (MFB) caused a greater reduction of NA and also decreased the DA and 5-HT content of the hypothalamus. Analysis of the PVN of the hypothalami of rats following 6-OHDA lesion of the MFB showed significantly decreased NA and 5-HT content. Neither DSP₄ treatment nor 6-OHDA lesion of the MFB affected the clonidine (250 g/kg, i.p.) induced stimulation of GH secretion. Injection of isoproterenol (1 mg/kg, i.p.) had varying effects on GH secretion. It stimulated GH release in control rats but not in DSP₄ or MFB lesioned rats. Direct injection of clonidine (0.1 g/l) into the PVN significantly stimulated GH secretion, whereas injection of isoproterenol (2.5 g/l) into the PVN did not affect GH levels when compared to controls. The results of the present study do not support the hypothesis that hypoactivity of the central noradrenergic system may be the cause of the blunted GH response to clonidine observed in depressed patients.     

The price of insulation: costs and benefits of feather delivery to nests for male tree swallows Tachycineta bicolor

Many species of birds line their nests with feathers, and it has been hypothesized that this functions to provide a thermally stable microenvironment for the development of eggs and nestlings. Feathers in the nest may also function as a mechanism for parasite control, providing a physical barrier that protects nestlings from ectoparasites. We tested these hypotheses by performing a feather removal and addition experiment in tree swallows Tachycineta bicolor, a species well‐known for lining their nests with feathers. While we found no evidence that quantity of feathers in nests influenced the ability of females to produce and incubate eggs, offspring in well‐feathered nests had longer flight feathers and were structurally larger just prior to fledging that those in nests with fewer feathers. Furthermore, we also demonstrated a positive correlation between feathers and the abundance of larval blow flies Protocalliphora spp. in nests, a result opposite to that predicted by the anti‐parasite hypothesis. While our study provides strong support for the insulation hypothesis, we also discuss the possibility that devoting time to feather gathering may result in males losing paternity in their nests, although manipulative studies will be necessary to fully evaluate this idea.     

Cytoskeletal involvement in spermiation and sperm transport

The process of spermiation and sperm transport was studied using specific inhibitors of cytoskeletal elements. Within 12-24 hr after the intratesticular injection of taxol, a compound that acts to stabilize microtubules and inhibit microtubule-related processes, an unusually large number of microtubules was seen within the body of the Sertoli cell. At the same time, transport of elements within the seminiferous epithelium was affected. At the end of stage VI of the cycle, step 19 spermatids were maintained in the deep recesses of the Sertoli cell and not transported to the rim of the seminiferous tubule lumen. At stage VIII, residual bodies remained at, or near, the rim of the tubule and were not transported to the base of the tubule. They underwent only partial degradation at this site, indicating that there may have been two phases involved in their dissolution--one autophagic and one phagocytic, but the latter did not occur since the residual bodies were not transported to Sertoli lysosomes at the base of the tubule. The observations suggest that microtubules are involved in transport processes within the seminiferous epithelium. Within 1-12 hr after the intratesticular injection of 500 microM cytochalasin D, a compound which interferes with actin-related processes, normal appearing tubulobulbar complexes were not present. The tubular portion (distal tube) of the complex did not initiate development. It was assumed that filaments (which were identified as such using NBD-phallacidin and the S-1 fragment of myosin) played an important role in the development of this portion of the complex. Cells did not eliminate cytoplasm normally, as evidenced by an enlarged cytoplasmic droplet, further emphasizing the published role for tubulobulbar complexes in cytoplasmic elimination. Although sperm were released normally from stage VIII tubules, many remained within the tubular lumen and did not traverse the duct system. Cytochalasin did not inhibit fluid secretion by the Sertoli cell, as demonstrated by efferent duct ligation, but did alter myoid cell actin cytoskeletal organization, suggesting that myoid cell contractility is primarily responsible for transport of sperm. Overall, the observations suggest that cytoskeletal activity of the Sertoli cell is important for several aspects of the spermiation process as well as sperm transport.     

Diversity of plant evolutionary lineages promotes arthropod diversity

Large‐scale habitat destruction and climate change result in the non‐random loss of evolutionary lineages, reducing the amount of evolutionary history represented in ecological communities. Yet, we have limited understanding of the consequences of evolutionary history on the structure of food webs and the services provided by biological communities. Drawing on 11 years of data from a long‐term plant diversity experiment, we show that evolutionary history of plant communities – measured as phylogenetic diversity – strongly predicts diversity and abundance of herbivorous and predatory arthropods. Effects of plant species richness on arthropods become stronger when phylogenetic diversity is high. Plant phylogenetic diversity explains predator and parasitoid richness as strongly as it does herbivore richness. Our findings indicate that accounting for evolutionary relationships is critical to understanding the severity of species loss for food webs and ecosystems, and for developing conservation and restoration policies.