MD studies of the DIS/DIS kissing complex solution and x-ray structures

As in all retroviruses, human immunodeficiency virus (HIV) genomic RNA is packaged into virions as a dimer. The two copies of the genome are noncovalently linked by their 5'-ends in the dimerization initiating site (DIS), which folds as a hairpin containing an apical autocomplementary sequence. In vitro, DIS is able to dimerize in two conformations: a kissing complex and an extended dimer. Both conformations have been resolved by NMR and x-ray diffraction. Here, we report molecular dynamics (MD) studies of the two available structures for the DIS/DIS kissing complex in aqueous solution and in the presence of sodium counterions. The two structures behave in two different manners. On one hand, the NMR structure displays a very stable behavior, and the simulated structure remains very close to the starting structure. On the other hand, the structure issued from crystallography displays a more dynamic behavior, in which residues A8 and A9 are seen in a new and surprising bulge-in conformation. The transition from the bulge-out to the bulge-in conformation is analyzed, and a new and simple dimerization process is proposed.     

Cryo-negative staining reveals conformational flexibility within yeast RNA polymerase I

The structure of the yeast DNA-dependent RNA polymerase I (RNA Pol I), prepared by cryo-negative staining, was studied by electron microscopy. A structural model of the enzyme at a resolution of 1.8 nm was determined from the analysis of isolated molecules and showed an excellent fit with the atomic structure of the RNA Pol II Delta4/7. The high signal-to-noise ratio (SNR) of the stained molecular images revealed a conformational flexibility within the image data set that could be recovered in three-dimensions after implementation of a novel strategy to sort the "open" and "closed" conformations in our heterogeneous data set. This conformational change mapped in the "wall/flap" domain of the second largest subunit (beta-like) and allows a better accessibility of the DNA-binding groove. This displacement of the wall/flap domain could play an important role in the transition between initiation and elongation state of the enzyme. Moreover, a protrusion was apparent in the cryo-negatively stained model, which was absent in the atomic structure and was not detected in previous 3D models of RNA Pol I. This structure could, however, be detected in unstained views of the enzyme obtained from frozen hydrated 2D crystals, indicating that this novel feature is not induced by the staining process. Unexpectedly, negatively charged molybdenum compounds were found to accumulate within the DNA-binding groove, which is best explained by the highly positive electrostatic potential of this region of the molecule, thus, suggesting that the stain distribution reflects the overall surface charge of the molecule.     

The structural bases of the processive degradation of iota-carrageenan, a main cell wall polysaccharide of red algae

iota-Carrageenans are sulfated 1,3-alpha-1,4-beta-galactans from the cell walls of red algae, which auto-associate into crystalline fibers made of aggregates of double-stranded helices. iota-Carrageenases, which constitute family 82 of glycoside hydrolases, fold into a right-handed beta-helix. Here, the structure of Alteromonas fortis iota-carrageenase bound to iota-carrageenan fragments was solved at 2.0A resolution (PDB 1KTW). The enzyme holds a iota-carrageenan tetrasaccharide (subsites +1 to +4) and a disaccharide (subsites -3, -4), thus providing the first direct determination of a 3D structure of iota-carrageenan. Electrostatic interactions between basic protein residues and the sulfate substituents of the polysaccharide chain dominate iota-carrageenan recognition. Glu245 and Asp247 are the proton donor and the base catalyst, respectively. C-terminal domain A, which was highly flexible in the native enzyme structure, adopts a alpha/beta-fold, also found in DNA/RNA-binding domains. In the substrate-enzyme complex, this polyanion-binding module shifts toward the beta-helix groove, forming a tunnel. Thus, from an open conformation which allows for the initial endo-attack of iota-carrageenan chains, the enzyme switches to a closed-tunnel form, consistent with its highly processive character, as seen from the electron-microscopy analysis of the degradation of iota-carrageenan fibers.     

Changes in the LHCI aggregation state during iron repletion in the unicellular red alga Rhodella violacea

Red algae are well suited to study the effects of iron deficiency on light-harvesting complex for photosystem I (LHCI), since they are totally devoid of light-harvesting complex for photosystem II (LHCII). Iron starvation results in a reduction of the pigment content, an increase of the fluorescence yield and a new emission band at 705 nm in the 77 K fluorescence emission spectra. These changes reflect the accumulation of uncoupled, aggregated LHCI in iron-depleted cells. Reconnection of LHCI to de novo synthesized reaction center I (RCI) is the first event, which takes place after iron addition. The changes in the aggregation state of LHCI are likely to occur also in brown and green algae.     

Tmevpg1, a candidate gene for the control of Theiler's virus persistence,could be implicated in the regulation of gamma interferon

The Tmevp3 locus controls the load of Theiler's virus RNA during persistent infection of the mouse central nervous system (CNS). We identified a candidate gene at this locus, Tmevpg1, by using a positional cloning approach. Tmevpg1 and its human ortholog, TMEVPG1, are expressed in the immune system and encode what appears to be a noncoding RNA. They are located in a cluster of cytokine genes that includes the genes for gamma interferon and one or two homolog of interleukin-10. We now report that Tmevpg1 is expressed in CNS-infiltrating immune cells of resistant B10.S mice, but not in those of susceptible SJL/J mice, following inoculation with Theiler's virus. The pattern of expression of Tmevpg1 is the same in B10.S mice and in SJL/J mice congenic for the resistant B10.S haplotype of Tmevp3. Nineteen polymorphisms were identified when the Tmevpg1 genes of B10.S and SJL/J mice were compared. Interestingly, Tmevpg1 is down regulated after in vitro stimulation of murine CD4(+) or CD8(+) splenocytes, whereas Ifng is up regulated. Similar patterns of expression of TMEVPG1 and IFNG were observed in human NK cells and CD4(+) and CD8(+) T lymphocytes. Therefore, Tmevpg1 is a strong candidate gene for the Tmevp3 locus and may be involved in the control of Ifng gene expression.     

Distribution of [14C]-trans-resveratrol,a cancer chemopreventive polyphenol,in mouse tissues after oral administration

Trans-resveratrol, a phenolic compound present in wine, has been reported to be a potential cancer chemopreventive agent. However, although it has numerous biological activities in vitro, there are few data about its bioavailability and tissue distribution in vivo. The objectives of this study were to investigate the absorption and tissue distribution of 14C-trans-resveratrol following oral administration to mice. Male Balb/c mice were given a single oral dose of 14C-trans-resveratrol and were sacrificed at 1.5, 3 or 6 h postdose. The distribution of radioactivity in tissues was evaluated using whole-body autoradiography, quantitative organ-level determination and microautoradiography. In addition, identification of radioactive compounds in kidney and liver was done with high-performance liquid chromatography. Autoradiographic survey of mice sections as well as radioactivity quantification in various organs revealed a preferential fixation of 14C-trans-resveratrol in the organs and biological liquids of absorption and elimination (stomach, liver, kidney, intestine, bile, urine). Moreover, we show that 14C-trans-resveratrol derived radioactivity is able to penetrate the tissues of liver and kidney, a finding supported by microautoradiography. The presence of intact 14C-trans-resveratrol together with glucurono- and/or sulfoconjugates in these tissues was also shown. This study demonstrates that trans-resveratrol is bioavailable following oral administration and remains mostly in intact form. The results also suggest a wide range of target organs for cancer chemoprevention by wine polyphenols in humans.     

Lysophosphatidic acid is a bioactive mediator in ovarian cancer

Lysophosphatidic acid (LPA) is a naturally occurring phospholipid that exhibits pleiotrophic biological activities, ranging from rapid morphological changes to long-term cellular effects such as induction of gene expression and stimulation of cell proliferation and survival on a wide spectrum of cell types. LPA binds and activates distinct members of the Edg/LP subfamily of G protein-coupled receptors that link to multiple G proteins including Gi, Gq and G12/13 to elicit cellular responses. LPA plays a critical role as a general growth, survival and pro-angiogenic factor, in the regulation of physiological and pathophysiological processes in vivo and in vitro. Our previous work indicates that abnormalities in LPA metabolism and function in ovarian cancer patients may contribute to the initiation and progression of the disease. Thus, LPA could be a potential target for cancer therapy. This review summarizes evidence that implicates LPA in the pathophysiology of human ovarian cancer and likely other types of human malignancies.     

Identification of XcpZ domains required for assembly of the secreton of Pseudomonas aeruginosa

Most of the exoproteins secreted by Pseudomonas aeruginosa are transported via the type II secretion system. This machinery, which is widely conserved in gram-negative bacteria, consists of 12 Xcp proteins organized as a multiprotein complex, also called the secreton. We previously reported that the mutual stabilization of XcpZ and XcpY plays an important role in the assembly of the secreton. In this study, we engineered variant XcpZ proteins by using linker insertion mutagenesis. We identified three distinct regions of XcpZ required for both the stabilization of XcpY and the functionality of the secreton. Interestingly, we also demonstrated that another component of the machinery, XcpP, can modulate the stabilizing activity of XcpZ on XcpY.