Ribosome loading onto the mRNA cap is driven by conformational coupling between eIF4G and eIF4E

The eukaryotic initiation factor 4G (eIF4G) is the core of a multicomponent switch controlling gene expression at the level of translation initiation. It interacts with the small ribosomal subunit interacting protein, eIF3, and the eIF4E/cap-mRNA complex in order to load the ribosome onto mRNA during cap-dependent translation. We describe the solution structure of the complex between yeast eIF4E/cap and eIF4G (393-490). Binding triggers a coupled folding transition of eIF4G (393-490) and the eIF4E N terminus resulting in a molecular bracelet whereby eIF4G (393-490) forms a right-handed helical ring that wraps around the N terminus of eIF4E. Cofolding allosterically enhances association of eIF4E with the cap and is required for maintenance of optimal growth and polysome distributions in vivo. Our data explain how mRNA, eIF4E, and eIF4G exists as a stable mRNP that may facilitate multiple rounds of ribosomal loading during translation initiation, a key determinant in the overall rate of protein synthesis.     

Model-based cap thickness and peak cap stress prediction for carotid MRI

A rupture-prone carotid plaque can potentially be identified by calculating the peak cap stress (PCS). For these calculations, plaque geometry from MRI is often used. Unfortunately, MRI is hampered by a low resolution, leading to an overestimation of cap thickness and an underestimation of PCS. We developed a model to reconstruct the cap based on plaque geometry to better predict cap thickness and PCS.We used histological stained plaques from 34 patients. These plaques were segmented and served as the ground truth. Sections of these plaques contained 93 necrotic cores with a cap thickness <0.62 mm which were used to generate a geometry-based model. The histological data was used to simulate in vivo MRI images, which were manually delineated by three experienced MRI readers. Caps below the MRI resolution (n = 31) were (digitally removed and) reconstructed according to the geometry-based model. Cap thickness and PCS were determined for the ground truth, readers, and reconstructed geometries.Cap thickness was 0.07 mm for the ground truth, 0.23 mm for the readers, and 0.12 mm for the reconstructed geometries. The model predicts cap thickness significantly better than the readers. PCS was 464 kPa for the ground truth, 262 kPa for the readers and 384 kPa for the reconstructed geometries. The model did not predict the PCS significantly better than the readers.The geometry-based model provided a significant improvement for cap thickness estimation and can potentially help in rupture-risk prediction, solely based on cap thickness. Estimation of PCS estimation did not improve, probably due to the complex shape of the plaques.     

Transmural exocytosis in maize root cap

Summary The maize root cap is a tissue known for its high production of a fucose-rich slime. At the cellular periphery, two kinds of components exist which are indistinguishable: the cell wall barrier and the slime which passes through. Two complementary probes were used, both at the light and the electron microscope level, in order to distinguish the different components. The lectinUlex europaeus agglutinin I was used as a probe targetting the slime and the enzyme cellulose 1,4--D-glucan cellobiohydrolase I was used to probe the cellulose framework. Both probes were used either alone or sequentially for double labeling. The cytochemical PATAg test was optionally used with the enzyme-gold complex labeling. After several technical improvements (multistep method, increase in accessibility), UeA I was used to follow the exocytic pathway of the slime from the Golgi apparatus to the exterior of the cell. The results indicate the occurrence of at least two populations of Golgi apparatus vesicles, and one is directly engaged in the transport of the fucoserich slime. The slime accumulated in pockets between the plasmamembrane and the outer tangential cell wall. The CBH I-gold complex showed the existence and the maintenance of a thin but continuous cellulosic layer, even when the cells slough. The double labeling showed the fucose-rich compounds within the cell wall. Data emphasize the role of the cell wall as a filtering barrier and a mechanical protection in the course of differentiation.Abbreviations CBH I EC 3.2.1.91, cellulose 1,4--D-glucan cellobiohydrolase I - CMC carboxymethyl cellulose - CPB citrate phosphate buffer - FITC fluorescein isothiocyanate - IC internal cell - PA-TAg periodic acid-thiocarbohydrazide-silver proteinate - PBS phosphate buffered saline - PC cell with accumulation pockets - PEG polyethyleneglycol - SC sloughed cell - UeA I Ulex europaeus agglutinin I - VI UeA I-labelled Golgi-derived vesicles - V2 UeA I-unlabelled Golgi-derived vesicles     

Geoperception in the lentil root cap

Previous analysis showed that, in its initial phase, the geotropic response of Lens culinaris L. roots cannot be explained by a simple action by sliding, pressure or contact of amyloplasts on a sensitive surface located along the longitudinal wall. In this study another mode of action is tested by considering the following parameters as functions of the roots inclination: (1) the distance (d) which the amyloplasts move; (2) their number of contacts (mean c) with parietal cytoplasm; (3) the variable (sin alpha) of the transversal component of the statolith weight (mean M x g sin alpha). It is shown that the initial rate of curvature (mean V), at the various angles, is related to the sedimentation of the amyloplasts by the equation mean V = a log b mean d mean c sin alpha (where a and b are constants). The results obtained prove that the geotropic stimulation is dependent upon the sine of the angle (alpha) of the root inclination and explain the sine rule deviation. The role of statoliths is discussed in the light of recent literature on growth inhibitors which are involved in the geotropic reaction.     

Endocytosis in maize root cap cells

Summary Primary roots of maize seedlings have been treated with solutions of lanthanum and lead salts in an attempt to demonstrate endocytosis. Subsurface cells in the root cap reveal deposits of these heavy metals in coated pits in the plasma membrane and in coated vesicles. In addition lead deposits were observed in coated evaginations (pits) on large (secretory) vesicles present at the trans-pole of the Golgi apparatus and on small vacuoles. Lead was also found in the peripheral regions of individual cisternae throughout the dictyosomal stack. We interpret our results as providing evidence for coated pit/coated vesicle-mediated endocytosis and for the direct recycling of plasma membrane to the Golgi apparatus.     

DNA conformational kinetics

A model for the time dependence of DNA conformational state probabilities is formulated in the form of first-order differential equations. This model is applied to investigate the renaturation and denaturation rates for T2 and T7 DNA as reported in the series of experiments by Record and Zimm. Qualitative agreement is found in denaturation and for series of renaturation experiments with the same initial condition. However, partial agreement with series of renaturation experiments having the same final condition is obtained only by including an initial bimolecular step with properly matched pairs of strands. Comparison of all experiments with the calculated rates yields 5 × 10⁴ min^?1 as the step rate for melting a single base pair.     

Protein conformational prediction

The prediction of the secondary and tertiary structure of globular and membrane proteins is reviewed. Prospects are encouraging for future developments, but present algorithms require cautious interpretation.     

Surface cap modifications in cold-treatedDrosophila melanogaster embryos

Summary When earlyDrosophila embryos were allowed to develop at 0°C, several abnormalities in the surface cap organization were observed. Scanning electron microscopy showed that exposure to cold mainly lead to the deformation of the cortical caps and to their partial fusion with adjacent caps. The process of cellularization was presumably affected and large uncellularized areas were observed. Rhodamine-phalloidin staining showed that cap deformation was closely related to the altered microfilament distribution, which was presumably responsible for the failure of large syncytial areas to cellularize. During the process of cellularization, F-actin localization did not depend on the microtubules forming the baskets around the elongating nuclei, but was related to the subpopulation of mictotubules radiating from the centrosomes toward the plasma membrane. Only these microtubules seemed to be affected by cold treatment.     

RNA conformational classes

RNA exhibits a large diversity of conformations. Three thousand nucleotides of 23S and 5S ribosomal RNA from a structure of the large ribosomal subunit were analyzed in order to classify their conformations. Fourier averaging of the six 3D distributions of torsion angles and analyses of the resulting pseudo electron maps, followed by clustering of the preferred combinations of torsion angles were performed on this dataset. Eighteen non-A-type conformations and 14 A-RNA related conformations were discovered and their torsion angles were determined; their Cartesian coordinates are available.     

Transcriptional analysis of the titin cap gene

Mutations in titin cap (Tcap), also known as telethonin, cause limb-girdle muscular dystrophy type 2G (LGMD2G). Tcap is one of the titin interacting Z-disc proteins involved in the regulation and development of normal sarcomeric structure. Given the essential role of Tcap in establishing and maintaining normal skeletal muscle architecture, we were interested in determining the regulatory elements required for expression of this gene in myoblasts. We have defined a highly conserved 421 bp promoter proximal promoter fragment that contains two E boxes and multiple putative Mef2 binding sequences. This promoter can be activated by MyoD and myogenin in NIH3T3 fibroblast cells, and maintains the differentiated cell-specific expression pattern of the endogenous Tcap in C2C12 cells. We find that while both E boxes are required for full activation by MyoD or myogenin in NIH3T3 cells, the promoter proximal E box has a greater contribution to activation of this promoter in C2C12 cells and to activation by MyoD in NIH3T3 cells. Together, the data suggest an important role for MyoD in activating Tcap expression through the promoter proximal E box. We also show that myogenin is required for normal expression in vivo and physically binds to the Tcap promoter during embryogenesis.