Stress granules: RNP-containing cytoplasmic bodies arising in stress: Structure and mechanism of organization

The review considers recent data on stress granules, which are dense RNP-containing cytoplasmic bodies that arise under stress conditions, e.g., in heat shock, UV irradiation, energy depletion, and oxidative stress. There is evidence that stress granules accumulate incomplete initiation complexes containing mRNA associated with proteins, small ribosomal subunits, and some translation initiation factors, and that stress granules are formed when cells are depleted of the ternary complex (eIF2-tRNA^Met-GTP), in particular, upon eIF2A phosphorylation or a decrease in GTP. Large ribosomal subunits and the ternary complex are absent from stress granules. The structural basis of stress granules is known. It is probable, however, that RNA-binding protein TIA-1, which normally occurs in the nucleus, forms prion-like aggregates that serve as scaffolds for other components of stress granules. The cytoskeleton facilitates the accumulation of stress granule components in local cytoplasmic sites. Studies of the formation and composition of stress granules are important for a better understanding of the regulation of translation initiation in vivo and the mechanisms of the cell response to stress factors.     

Functions of maternal mRNA in early development

In this review, the types of mRNAs found in oocytes and eggs of several animal species, particularly Drosophila, marine invertebrates, frogs, and mice, are described. The roles that proteins derived from these mRNAs play in early development are discussed, and connections between maternally inherited information and embryonic pattern are sought. Comparisons between genetically identified maternally expressed genes in Drosophila and maternal mRNAs biochemically characterized in other species are made when possible. Regulation of the meiotic and early embryonic cell cycles is reviewed, and translational control of maternal mRNA following maturation and/or fertilization is discussed with regard to specific mRNAs.     

Strong association between mRNA folding strength and protein abundance in S. cerevisiae

One of the open questions in regulatory genomics is how the efficiency of gene translation is encoded in the coding sequence. Here we analyse recently generated measurements of folding energy in Saccharomyces cerevisiae, showing that genes with high protein abundance tend to have strong mRNA folding (mF; R=0.68). mF strength also strongly correlates with ribosomal density and mRNA levels, suggesting that this relation at least partially pertains to the efficiency of translation elongation, presumably by preventing aggregation of mRNA molecules.     

Analyzing and enhancing mRNA translational efficiency in an Escherichia coli in vitro expression system

The dependence of efficiency of translation initiation on mRNA sequence parameters was investigated in an Escherichia coli in vitro expression system. We designed a large-scale expression experiment focussing on the influence of sequence variations in the translated region (TR) of the mRNA without changing the 5'-untranslated region (5'-UTR). The level of translated protein from 756 expression constructs was measured and the influence of a large number of possible effector attributes was statistically analyzed. Base exchanges immediately adjacent to the start codon up to nucleotide (+)25 had a profound effect on translational efficiency. Correlation analysis revealed a significant dependence on base pair probability and G+C content on the expression level, indicating that mRNA secondary structure in this region hampers translation. Using our training data, we developed a methodology to predict and improve the translation efficiency of open reading frames (ORFs).     

The efficiency of different IRESs (Internal Ribosomes Entry Site) in monocistronic mRNAS

The IRES from poliovirus and from encephalomyocarditis virus (EMCV) added between the cap and the AUG initiator codon were strong inhibitors of chloramphenicol acetyltransferase gene expression in three different cell types. The poliovirus IRES also inhibited bGH (bovine growth hormone) cDNA expression in the HC11 mammary cell line when added between the rabbit whey acidic gene promoter and the cDNA whereas the HTLV-1 IRES showed a stimulatory effect in the same situation. RNA stem loops were added before HTLV-1 (SUR) and the BiP (Immunoglobulin heavy-chain Binding Protein) IRESs followed by the firefly luciferase gene under the control of Rous sarcoma virus (RSV) promoter. The RNA loops abolished the expression of the reporter gene almost completely. These data suggest that the different IRESs may favour or inhibit translation of monocistronic mRNA.     

Comparative analysis of the kinetics and dynamics of K10, bicoid,and oskar mRNA localization in the Drosophila oocyte

The localization of mRNAs to discrete cytoplasmic sites is important for the function of many, and perhaps all, cells. Many mRNAs are thought to be localized in a directed fashion along microtubule tracts. This appears to be the case for several mRNAs that are synthesized in Drosophila nurse cells and then transported into, and localized within, the oocyte. In this report, we compare the transport/localization kinetics and dynamics of three such mRNAs, K10, bicoid, and oskar. We generated flies carrying heat shock—K10, -bicoid, or -oskar fusion genes, which allowed us to carry out the molecular genetics equivalent of a pulse chase experiment. Our analyses indicate that K10, bicoid, and oskar mRNA transport and localization are a continuous process involving multiple movements of the same mRNA molecules. The transport and early localization dynamics of the three mRNAs are indistinguishable from each other and, in order, include accumulation in the apical regions of nurse cells, transport to the posterior pole of the oocyte, and movement to the oocyte's anterior cortex at stage 8. We also show that the rate of transport is the same in each case, ∼︁1.1 μm/min. Only after stage 8 are RNA-specific movements seen The similarities in the transport/early localization kinetics and dynamics of K10, bicoid, and oskar mRNAs suggest that such events are mediated by a common set of factors. We also observe that all three mRNAs localize to the apical regions of somatic follicle cells when expressed in such cells, suggesting that the transport/early localization factors are widespread and involved in the localization of mRNAs in many tissues. © 1996 Wiley-Liss, Inc.     

Single-Molecule Imaging of mRNA Localization and Regulation during the Integrated Stress Response

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