Linkage of the β-Like ω-Globin Gene to α-Like Globin Genes in an Australian Marsupial Supports the Chromosome Duplication Model for Separation of Globin Gene Clusters

The structure, function, and evolutionary history of globin genes have been the subject of extensive investigation over a period of more than 40 years, yet new globin genes with highly specialized functions are still being discovered and much remains uncertain about their evolutionary history. Here we investigate the molecular evolution of the -globin gene family in a marsupial species, the tammar wallaby, Macropus eugenii. We report the complete DNA sequences of two -like globin genes and show by phylogenetic analyses that one of these genes is orthologous to embryonically expressed -globin genes of marsupials and eutherians and the other is orthologous to adult expressed -globin genes of marsupials and eutherians. We show that the tammar wallaby contains a third functional -like globin gene, -globin, which forms part of the -globin gene cluster. The position of -globin on the 3 side of the -globin cluster and its ancient phylogenetic history fit the criteria, originally proposed by Jeffreys et al. (1980), of a fossil -globin gene and suggest that an ancient chromosome or genome duplication preceded the evolution of unlinked clusters of - and -globin genes in mammals and avians. In eutherian mammals, such as humans and mice, -globin has been silenced or translocated away from the -globin locus, while in marsupials -globin is coordinately expressed with the adult -globin gene just prior to birth to produce a functional hemoglobin (_{2 2}).     

Dynamic release of Cdc34 from SCF. the hand that rocks the cradle

Polyubiquitylation is a complex but poorly understood biochemical reaction catalyzed by E3 ubiquitin ligases. In this issue of Cell, Deffenbaugh et al. provide experimental support for a model in which the dynamic release of the ubiquitin-charged E2 Cdc34 from its primary binding site within the rigid cradle-like SCF E3 complex allows for unexpected spatial flexibility to assemble a polyubiquitin chain.     

Non-stochastic and stochastic linear indices of the 'molecular pseudograph's atom adjacency matrix': application to 'in silico' studies for the rational discovery of new antimalarial compounds

Malaria is one of the most deadly diseases, affecting million of people especially in developing countries. Because of the rapidly increasing threat worldwide of malaria epidemics multidrugs resistant to therapies, there is an urgent global need to discover new classes of antimalarial compounds. In an effort to overcome this problem, we have investigated the use of structure-based classification models for the 'rational' selection/identification or design/optimization of new lead antimalarials from virtual combinatorial data sets. In this sense, TOpological MOlecular COMputer Design strategy (TOMOCOMD approach) has been introduced in order to obtain two quantitative models for the discrimination of antimalarials. A collected data set containing 597 antimalarial compounds is presented as a helpful tool not only for theoretical chemist but for other researchers in this area. The validated models (including non-stochastic and stochastic indices) classify correctly more than 90% of compounds in both training and external prediction data sets. They showed high Matthews' correlation coefficients; 0.87 and 0.82 for training and 0.86 and 0.79 for test set. The TOMOCOMD-CARDD approach implemented in this work was successfully compared with two of the most useful models for antimalarials selection reported so far. Thus we expect that these two QSAR models can be used in the identification of previously un-known antimalarials compounds.     

Tropolysin, a new oligopeptidase from African trypanosomes

Oligopeptidases are emerging as important pathogenic factors and therapeutic targets in trypanosome infections. We describe here the purification, cloning, and biochemical analysis of a new oligopeptidase from two pathogenic African trypanosomes. This oligopeptidase, which we have called tropolysin (encoded by the trn gene), represents an evolutionarily distant member of the M3A subfamily of metallopeptidases, ancestral to thimet oligopeptidase, neurolysin, and saccharolysin. The trn gene was present as a single copy per haploid genome, was expressed in both the mammalian and insect stages of the parasite life cycle, and encoded an 84 kDa protein. Both purified and hyperexpressed tropolysin hydrolyzed bradykinin-derived fluorogenic peptide substrates at restricted sites, with an alkaline pH optimum, and were activated by dithiothreitol and reduced glutathione and by divalent metal cations, in the order Zn(2+) > Co(2+) > Mn(2+). Under oxidizing conditions, tropolysin reversibly formed inactive multimers. Tropolysin exhibited a preference for acidic amino acid side chains in P(4), hydrophobic side chains in P(3), and hydrophobic or large uncharged side chains in P(1), P(1)', and P(3)', while the S(2)' site was unselective. Highly charged residues were not tolerated in P(1)'. Tropolysin was responsible for the bulk of the kinin-degrading activity in trypanosome lysates, potently (k(cat) approximately 119 s(-)(1)) inactivated the vasoactive kinins bradykinin and kallidin, and generated angiotensin(1-7) from angiotensin I. This hydrolysis both abolished the capacity of bradykinin to stimulate the bradykinin B(2) receptor and abrogated bradykinin prohypotensive properties in vivo, raising the possibility that tropolysin may play a role in the dysregulated kinin metabolism observed in the plasma of trypanosome-infected hosts.     

Tissue-specific, inducible, and hormonal control of the human UDP-glucuronosyltransferase-1 (UGT1) locus

The human UDP-glucuronosyltransferase 1 (UGT1) locus spans nearly 200 kb on chromosome 2 and encodes nine UGT1A proteins that play a prominent role in drug and xenobiotic metabolism. Transgenic UGT1 (Tg-UGT1) mice have been created, and it has been demonstrated that tissue-specific and xenobiotic receptor control of the UGT1A genes is influenced through circulating humoral factors. In Tg-UGT1 mice, the UGT1A proteins are differentially expressed in the liver and gastrointestinal tract. Gene expression profiles confirmed that all of the UGT1A genes can be targeted for regulation by the pregnane X receptor activator pregnenolone-16alpha-carbonitrile (PCN) or the Ah receptor ligand 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). In addition, the selective induction of glucuronidation activity toward lamotrigine, ethinyl estradiol, chenodeoxycholic acid, and lithocholic acid by either PCN or TCDD in small intestine from Tg-UGT1 mice corresponded to expression of the locus in this tissue. Induction of UGT1A1 by PCN and TCDD is believed to be highly dependent upon glucocorticoids, because submicromolar concentrations of dexamethasone actively promote PCN and TCDD induction of UGT1A1 in Tg-UGT1 primary hepatocytes. The role of hormonal control of the UGT1 locus was further verified in pregnant and nursing Tg-UGT1 mice. In maternal 14-day post-conception Tg-UGT1mice, liver UGT1A1, UGT1A4, and UGT1A6 were induced, with the levels returning to near normal by birth. However, maternal liver UGT1A4 and UGT1A6 were dramatically elevated and maintained after birth, indicating that these proteins may play a critical role in maternal metabolism during lactation. With expression of the UGT1 locus confirmed in a variety of mouse tissues, these results suggested that the Tg-UGT1 mice will be a useful model to examine the regulatory and functional properties of human glucuronidation.     

Metagenomic gene discovery: past, present and future

It is now widely accepted that the application of standard microbiological methods for the recovery of microorganisms from the environment has had limited success in providing access to the true extent of microbial biodiversity. It follows that much of the extant microbial genetic diversity (collectively termed the metagenome) remains unexploited, an issue of considerable relevance to a wider understanding of microbial communities and of considerable importance to the biotechnology industry. The recent development of technologies designed to access this wealth of genetic information through environmental nucleic acid extraction has provided a means of avoiding the limitations of culture-dependent genetic exploitation.     

New directions in incidence-dose modeling

Many cellular responses are quantal; that is, they either take place or they do not. Examples of "either-or" responses include cell replication, differentiation and apoptosis. Surprisingly, induction of suites of genes and coordinated phenotypic changes in cells are also often quantal, where embedded molecular circuitry creates on-off switches. Mechanistic incidence-dose (ID) models need to account for the quantal characteristics of cellular switches that contribute, in turn, to dose thresholds and to the incidence of biological responses in individuals. Interdisciplinary systems biology approaches create mechanistic ID models based on: (i) detailed knowledge of the cellular circuitry controlling signal transduction; (ii) evolving biological modeling tools describing cellular circuits and their perturbations by chemicals and (iii) high throughput, high coverage "omic" screens for examining cell signaling pathways and biological responses. These interdisciplinary approaches should produce novel, quantitative ID models for biological responses and greatly improve the biological basis of safety and risk assessments.