Hemoprotein time-resolved X-ray crystallography

In the last decade the role of structural dynamics in controlling protein function was actively investigated using new and advanced experimental approaches. In particular, time resolved crystallography, despite some practical difficulties, is being used extensively to complement the study of protein structure-function relationships with information on the dynamics, based on experimental evidence. Here we present a short overview of the results obtained on dynamical properties of myoglobin and homologous hemoproteins, where the photosensitive heme-Fe--ligand bond has allowed transient intermediates to be studied by different flash photolysis methods coupled to Laue X-ray diffraction, thus highlighting some of the dynamical events that characterize diffusion of a diatomic ligand to/from the heme in model hemoproteins.     

Crystal structure of a methyltransferase from a no-known-vector Flavivirus

Presently known flaviviruses belong to three major evolutionary branches: tick-borne viruses, mosquito-borne viruses and viruses with no known vector. Here we present the crystal structure of the Yokose virus methyltransferase at 1.7 Å resolution, the first structure of a methyltransferase of a Flavivirus with no known vector. Structural comparison of three methyltransferases representative of each of the Flavivirus branches shows that fold and structures are closely conserved, most differences being related to surface loops flexibility. Analysis of the conserved residues throughout all the sequenced flaviviral methyltransferases reveals that, besides the central cleft hosting the substrate and cofactor binding sites, a second, almost continuous, patch is conserved and points away from active site towards the back of the protein. The high level of structural conservation in this region could be functional for the methyltransferase/RNA interaction and stabilization of the ensuing complex.     

Recognition of RNA cap in the Wesselsbron virus NS5 methyltransferase domain: implications for RNA-capping mechanisms in Flavivirus

The mRNA-capping process starts with the conversion of a 5′-triphosphate end into a 5′-diphosphate by an RNA triphosphatase, followed by the addition of a guanosine monophosphate unit in a 5′-5′ phosphodiester bond by a guanylyltransferase. Methyltransferases are involved in the third step of the process, transferring a methyl group from S-adenosyl-l-methionine to N7-guanine (cap 0) and to the ribose 2′OH group (cap 1) of the first RNA nucleotide; capping is essential for mRNA stability and proper replication. In the genus Flavivirus, N7-methyltransferase and 2′O-methyltransferase activities have been recently associated with the N-terminal domain of the viral NS5 protein. In order to further characterize the series of enzymatic reactions that support capping, we analyzed the crystal structures of Wesselsbron virus methyltransferase in complex with the S-adenosyl-l-methionine cofactor, S-adenosyl-l-homocysteine (the product of the methylation reaction), Sinefungin (a molecular analogue of the enzyme cofactor), and three different cap analogues (GpppG, ^N7MeGpppG, and ^N7MeGpppA). The structural results, together with those on other flaviviral methyltransferases, show that the capped RNA analogues all bind to an RNA high-affinity binding site. However, lack of specific interactions between the enzyme and the first nucleotide of the RNA chain suggests the requirement of a minimal number of nucleotides following the cap to strengthen protein/RNA interaction. Our data also show that, following incubation with guanosine triphosphate, Wesselsbron virus methyltransferase displays a guanosine monophosphate molecule covalently bound to residue Lys28, hinting at possible implications for the transfer of a guanine group to ppRNA. The structures of the Wesselsbron virus methyltransferase complexes obtained are discussed in the context of a model for N7-methyltransferase and 2′O-methyltransferase activities.     

Responding to chromosomal breakage during M-phase: insights from a cell-free system

DNA double strand breaks (DSBs) activate ATM and ATR dependent checkpoints that prevent the onset of mitosis. However, how cells react to DSBs occurring when they are already in mitosis is poorly understood. The Xenopus egg extract has been utilized to study cell cycle progression and DNA damage checkpoints. Recently this system has been successfully used to uncover an ATM and ATR dependent checkpoint affecting centrosome driven spindle assembly. These studies have led to the identification of XCEP63 as major target of this pathway. XCEP63 is a coiled-coil rich protein localized at centrosome essential for proper spindle assembly. ATM and ATR directly phosphorylate XCEP63 on serine 560 inducing its delocalization from centrosome, which in turn delays spindle assembly. This pathway might contribute to regulate DNA repair or mitotic cell survival in the presence of chromosome breakage.     

Influenza Outbreak during Sydney World Youth Day 2008: The Utility of Laboratory Testing and Case Definitions on Mass Gathering Outbreak Containment

Background

Influenza causes annual epidemics and often results in extensive outbreaks in closed communities. To minimize transmission, a range of interventions have been suggested. For these to be effective, an accurate and timely diagnosis of influenza is required. This is confirmed by a positive laboratory test result in an individual whose symptoms are consistent with a predefined clinical case definition. However, the utility of these clinical case definitions and laboratory testing in mass gathering outbreaks remains unknown.

Methods and Results

An influenza outbreak was identified during World Youth Day 2008 in Sydney. From the data collected on pilgrims presenting to a single clinic, a Markov model was developed and validated against the actual epidemic curve. Simulations were performed to examine the utility of different clinical case definitions and laboratory testing strategies for containment of influenza outbreaks. Clinical case definitions were found to have the greatest impact on averting further cases with no added benefit when combined with any laboratory test. Although nucleic acid testing (NAT) demonstrated higher utility than indirect immunofluorescence antigen or on-site point-of-care testing, this effect was lost when laboratory NAT turnaround times was included. The main benefit of laboratory confirmation was limited to identification of true influenza cases amenable to interventions such as antiviral therapy.

Conclusions

Continuous re-evaluation of case definitions and laboratory testing strategies are essential for effective management of influenza outbreaks during mass gatherings.     

Intratumor heterogeneity in evolutionary models of tumor progression

With rare exceptions, human tumors arise from single cells that have accumulated the necessary number and types of heritable alterations. Each such cell leads to dysregulated growth and eventually the formation of a tumor. Despite their monoclonal origin, at the time of diagnosis most tumors show a striking amount of intratumor heterogeneity in all measurable phenotypes; such heterogeneity has implications for diagnosis, treatment efficacy, and the identification of drug targets. An understanding of the extent and evolution of intratumor heterogeneity is therefore of direct clinical importance. In this article, we investigate the evolutionary dynamics of heterogeneity arising during exponential expansion of a tumor cell population, in which heritable alterations confer random fitness changes to cells. We obtain analytical estimates for the extent of heterogeneity and quantify the effects of system parameters on this tumor trait. Our work contributes to a mathematical understanding of intratumor heterogeneity and is also applicable to organisms like bacteria, agricultural pests, and other microbes.     

Physiological changes in major soldiers of Macrotermes gilvus (Isoptera: Termitidae) induced by the endoparasitoid Misotermes mindeni (Diptera: Phoridae)

The majority of true parasitoids manipulate their host’s physiology for their own benefit. In this study, we documented the physiological changes that occurred in major soldiers of the subterranean termite Macrotermes gilvus (Hagen) (Isoptera: Termitidae) parasitized by the koinobiont larval endoparasitoid Misotermes mindeni Disney and Neoh (Diptera: Phoridae). We compared the metabolic rate, body water content, body water loss rate, cuticular permeability, and desiccation tolerance between parasitized and unparasitized major soldiers. The metabolic rate of parasitized hosts was significantly higher than that of unparasitized termites. Mean total body water content of parasitized major soldiers (64.73 ± 3.26%) was significantly lower than that of unparasitized termites (71.99 ± 2.23%). Parasitized hosts also had significantly lower total body water loss rates (5.72 ± 0.06%/h) and higher cuticular permeability (49.37 ± 11.26 μg/cm/h/mmHg) than unparasitized major soldiers (6.75 ± 0.16%/h and 60.76 ± 24.98 μg/cm/h/mmHg, respectively). Parasitized major soldiers survived almost twice as long as unparasitized termites (LT₅₀ = 6.66 h and LT₅₀ = 3.40 h, respectively) and they had significantly higher tolerance to water loss compared to unparasitized termites (45.28 ± 6.79% and 32.84 ± 7.69%, respectively). Body lipid content in parasitized hosts (19.84 ± 6.27%) was significantly higher than that of unparasitized termites (6.17 ± 7.87%). Finally, parasitized hosts had a significantly lower percentage of cuticular water content than unparasitized major soldiers (10.97 ± 1.84% and 13.17 ± 2.21%, respectively). Based on these data, we conclude that the parasitism-induced physiological changes in the host are beneficial to the parasitoids as the alterations can clearly increase the parasite’s chances of survival when exposed to extreme environmental conditions and ensure that the parasitoids are able to complete their larval development successfully before the host dies.