The microenvironment dictates glycocalyx construction and immune surveillance.

Efforts to identify anti-cancer therapeutics and understand tumor-immune interactions are built with models that do not match the microenvironmental characteristics of human tissues. Using models which mimic the physical properties of healthy or cancerous tissues and a physiologically relevant culture medium, we demonstrate that the chemical and physical properties of the microenvironment regulate the composition and topology of the glycocalyx. Remarkably, we find that cancer and age-related changes in the physical properties of the microenvironment are sufficient to adjust immune surveillance via the topology of the glycocalyx, a previously unknown phenomenon observable only with a physiologically relevant culture medium.

RGG motif proteins: modulators of mRNA functional states.

A recent report demonstrates that a subset of RGG-motif proteins can bind translation initiation factor eIF4G and repress mRNA translation. This adds to the growing number of roles RGG-motif proteins play in modulating transcription, splicing, mRNA export and now translation. Herein, we review the nature and breadth of functions of RGG-motif proteins.

P-bodies and stress granules: possible roles in the control of translation and mRNA degradation.

The control of translation and mRNA degradation is important in the regulation of eukaryotic gene expression. In general, translation and steps in the major pathway of mRNA decay are in competition with each other. mRNAs that are not engaged in translation can aggregate into cytoplasmic mRNP granules referred to as processing bodies (P-bodies) and stress granules, which are related to mRNP particles that control translation in early development and neurons.

Stm1 modulates translation after 80S formation in Saccharomyces cerevisiae.

The control of translation is a critical aspect of gene regulation. It is often inversely related to mRNA degradation and is typically controlled during initiation. The Stm1 protein in Saccharomyces cerevisiae has been shown to interact with ribosomes, affect the interaction of eEF3 with ribosomes, and promote the decapping of a subclass of mRNAs.

Analyzing P-bodies and stress granules in Saccharomyces cerevisiae.

Eukaryotic cells contain at least two types of cytoplasmic RNA-protein (RNP) granules that contain nontranslating mRNAs. One such RNP granule is a P-body, which contains translationally inactive mRNAs and proteins involved in mRNA degradation and translation repression. A second such RNP granule is a stress granule which also contains mRNAs, some RNA binding proteins and several translation initiation factors, suggesting these granules contain mRNAs stalled in translation initiation.

Identification and analysis of the interaction between Edc3 and Dcp2 in Saccharomyces cerevisiae.

Cap hydrolysis is a critical control point in the life of eukaryotic mRNAs and is catalyzed by the evolutionarily conserved Dcp1-Dcp2 complex. In Saccharomyces cerevisiae, decapping is modulated by several factors, including the Lsm family protein Edc3, which directly binds to Dcp2. We show that Edc3 binding to Dcp2 is mediated by a short peptide sequence located C terminal to the catalytic domain of Dcp2.

Analysis of Dom34 and its function in no-go decay.

Eukaryotic mRNAs are subject to quality control mechanisms that degrade defective mRNAs. In yeast, mRNAs with stalls in translation elongation are targeted for endonucleolytic cleavage by No-Go decay (NGD). The cleavage triggered by No-Go decay is dependent on Dom34p and Hbs1p, and Dom34 has been proposed to be the endonuclease responsible for mRNA cleavage.

Analyzing P-bodies in Saccharomyces cerevisiae.

Cytoplasmic processing bodies, or P-bodies, are RNA-protein granules found in eukaryotic cells. P-bodies contain non-translating mRNAs and proteins involved in mRNA degradation and translational repression. P-bodies, and the mRNPs within them, have been implicated in mRNA storage, mRNA degradation, and translational repression.

Analysis of cytoplasmic mRNA decay in Saccharomyces cerevisiae.

The yeast, Saccharomyces cerevisiae, is a model system for the study of eukaryotic mRNA degradation. In this organism, a variety of methods have been developed to measure mRNA decay rates, trap intermediates in the mRNA degradation process, and establish precursor-product relationships. In addition, the use of mutant strains lacking specific enzymes involved in mRNA destruction, or key regulatory proteins, allows one to determine the mechanisms by which individual mRNAs are degraded.

CGH-1 and the control of maternal mRNAs.

Development requires the translation of stored maternal messenger RNAs (mRNAs) in a spatial and temporally specified manner. Maternal mRNAs are often in large RNA-protein (RNP) granules. Recent papers reveal that maternal mRNA granules in Caenorhabditis elegans oocytes and early development are dynamic and related to P-bodies and stress granules, which are conserved RNP granules seen in somatic cells.

Stm1 modulates mRNA decay and Dhh1 function in Saccharomyces cerevisiae.

The control of mRNA degradation and translation are important for the regulation of gene expression. mRNA degradation is often initiated by deadenylation, which leads to decapping and 5'-3' decay. In the budding yeast Saccharomyces cerevisae, decapping is promoted by the Dhh1 and Pat1 proteins, which appear to both inhibit translation initiation and promote decapping.

Stressed out? Make some modifications!

Stress granules and processing bodies are related mRNA-containing granules implicated in controlling mRNA translation and decay. A genomic screen identifies numerous factors affecting granule formation, including proteins involved in -GlcNAc modifications. These results highlight the importance of post-translational modifications in translational control and mRNP granule formation.

Computational analysis of miRNA-mediated repression of translation: implications for models of translation initiation inhibition.

The mechanism by which miRNAs inhibit translation has been under scrutiny both in vivo and in vitro. Divergent results have led to the suggestion that miRNAs repress translation by a variety of mechanisms including blocking the function of the cap in stimulating translation. However, these analyses largely only examine the final output of the multistep process of translation.

Pat1 contains distinct functional domains that promote P-body assembly and activation of decapping.

The control of mRNA degradation and translation are important aspects of gene regulation. Recent results suggest that translation repression and mRNA decapping can be intertwined and involve the formation of a quiescent mRNP, which can accumulate in cytoplasmic foci referred to as P bodies. The Pat1 protein is a key component of this complex and an important activator of decapping, yet little is known about its function.

RNA quality control in eukaryotes.

Eukaryotic cells contain numerous RNA quality-control systems that are important for shaping the transcriptome of eukaryotic cells. These systems not only prevent accumulation of nonfunctional RNAs but also regulate normal mRNAs, repress viral and parasitic RNAs, and potentially contribute to the evolution of new RNAs and hence proteins. These quality-control circuits can be viewed as a series of kinetic competitions between steps in normal RNA biogenesis or function and RNA degradation pathways.

Edc3p and a glutamine/asparagine-rich domain of Lsm4p function in processing body assembly in Saccharomyces cerevisiae.

Processing bodies (P-bodies) are cytoplasmic RNA granules that contain translationally repressed messenger ribonucleoproteins (mRNPs) and messenger RNA (mRNA) decay factors. The physical interactions that form the individual mRNPs within P-bodies and how those mRNPs assemble into larger P-bodies are unresolved. We identify direct protein interactions that could contribute to the formation of an mRNP complex that consists of core P-body components.

Analysis of P-body assembly in Saccharomyces cerevisiae.

Recent experiments have defined cytoplasmic foci, referred to as processing bodies (P-bodies), that contain untranslating mRNAs in conjunction with proteins involved in translation repression and mRNA decapping and degradation. However, the order of protein assembly into P-bodies and the interactions that promote P-body assembly are unknown. To gain insight into how yeast P-bodies assemble, we examined the P-body accumulation of Dcp1p, Dcp2p, Edc3p, Dhh1p, Pat1p, Lsm1p, Xrn1p, Ccr4p, and Pop2p in deletion mutants lacking one or more P-body component.

Cytoplasmic decay of intergenic transcripts in Saccharomyces cerevisiae.

Eukaryotes produce a number of noncoding transcripts from intergenic regions. In Saccharomyces cerevisiae, such cryptic unstable transcripts (CUTs) are thought to be degraded in the nucleus by a process involving polyadenylation and 3'-to-5' degradation by the nuclear exosome. In this work, we examine the degradation pathway of the RNA SRG1, which is produced from an intergenic region and contributes to the regulation of the SER3 gene by promoter occlusion during SRG1 transcription.

Translation-independent inhibition of mRNA deadenylation during stress in Saccharomyces cerevisiae.

Post-transcriptional control mechanisms play an important role in regulating gene expression during cellular responses to stress. For example, many stresses inhibit translation, and at least some stresses inhibit mRNA turnover in yeast and mammalian cells. We show that hyperosmolarity, heat shock, and glucose deprivation stabilize multiple mRNAs in yeast, primarily through inhibition of deadenylation.

CAR-1 and trailer hitch: driving mRNP granule function at the ER?

The targeting of messenger RNAs (mRNAs) to specific subcellular sites for local translation plays an important role in diverse cellular and developmental processes in eukaryotes, including axis formation, cell fate determination, spindle pole regulation, cell motility, and neuronal synaptic plasticity. Recently, a new conserved class of Lsm proteins, the Scd6 family, has been implicated in controlling mRNA function. Depletion or mutation of members of the Scd6 family, Caenorhabditis elegans CAR-1 and Drosophila melanogaster trailer hitch, lead to a variety of developmental phenotypes, which in some cases can be linked to alterations in the endoplasmic reticulum (ER).

Beta-catenin is essential for pancreatic acinar but not islet development.

Despite our increasingly sophisticated understanding of transcriptional regulation in pancreas development, we know relatively little about the extrinsic signaling pathways involved in this process. We show here that the early pancreatic epithelium exhibits a specific enrichment in unphosphorylated beta-catenin protein, a hallmark of activation of the canonical Wnt signaling pathway. To determine if this pathway is functionally required for normal pancreas development, we have specifically deleted the beta-catenin gene in these cells.

Movement of eukaryotic mRNAs between polysomes and cytoplasmic processing bodies.

Eukaryotic cells contain nontranslating messenger RNA concentrated in P-bodies, which are sites where the mRNA can be decapped and degraded. We present evidence that mRNA molecules within yeast P-bodies can also return to translation. First, inhibiting delivery of new mRNAs to P-bodies leads to their disassembly independent of mRNA decay.

Adult pancreatic beta-cells are formed by self-duplication rather than stem-cell differentiation.

How tissues generate and maintain the correct number of cells is a fundamental problem in biology. In principle, tissue turnover can occur by the differentiation of stem cells, as is well documented for blood, skin and intestine, or by the duplication of existing differentiated cells. Recent work on adult stem cells has highlighted their potential contribution to organ maintenance and repair.

Identification of Edc3p as an enhancer of mRNA decapping in Saccharomyces cerevisiae.

The major pathway of mRNA decay in yeast initiates with deadenylation, followed by mRNA decapping and 5'-3' exonuclease digestion. An in silico approach was used to identify new proteins involved in the mRNA decay pathway. One such protein, Edc3p, was identified as a conserved protein of unknown function having extensive two-hybrid interactions with several proteins involved in mRNA decapping and 5'-3' degradation including Dcp1p, Dcp2p, Dhh1p, Lsm1p, and the 5'-3' exonuclease, Xrn1p.