Single-molecule visualization of mRNA circularization during translation

Translation is mediated by precisely orchestrated sequential interactions among translation initiation components, mRNA, and ribosomes. Biochemical, structural, and genetic techniques have revealed the fundamental mechanism that determines what occurs and when, where and in what order. Most mRNAs are circularized via the eIF4E–eIF4G–PABP interaction, which stabilizes mRNAs and enhances translation by recycling ribosomes. However, studies using single-molecule fluorescence imaging have allowed for the visualization of complex data that opposes the traditional “functional circularization” theory. Here, we briefly introduce single-molecule techniques applied to studies on mRNA circularization and describe the results of in vitro and live-cell imaging. Finally, we discuss relevant insights and questions gained from single-molecule research related to translation.Subject terms: Single-molecule biophysics, Ribosome     

mRNA transport to and translation in neuronal dendrites

Transport of mRNA is an important biological process in all cells that sets up gradients of translated protein from the site of mRNA docking and translation. Neurons are highly polarized cells where the targeted movement of RNAs and local translation at that site have been shown to be integral to the proper functioning of the neuron. Indeed, this specialized biological function for localized RNAs in particular neurons may in part confer a selective advantage on these cells such that they "out-compete" others in the race to establish synaptic connectivity. In this mini-review we highlight some of the salient features of RNA targeting and translation in neurons.     

Inhibition of cell proliferation by a resveratrol analog in human pancreatic and breast cancer cells

Resveratrol has been reported to possess cancer preventive properties. In this study, we analyzed anti-tumor activity of a newly synthesized resveratrol analog, cis-3,4'',5-trimethoxy-3''-hydroxystilbene (hereafter called 11b) towards breast and pancreatic cancer cell lines. 11b treatments reduced the proliferation of human pancreatic and breast cancer cells, arrested cells in the G2/M phase, and increased the percentage of cells in the subG1/G0 fraction. The 11b treatments also increased the total levels of mitotic checkpoint proteins such as BubR1, Aurora B, Cyclin B, and phosphorylated histone H3. Mechanistically, 11b blocks microtubule polymerization in vitro and it disturbed microtubule networks in both pancreatic and breast cancer cell lines. Computational modeling of the 11b-tubulin interaction indicates that the dimethoxyphenyl group of 11b can bind to the colchicine binding site of tubulin. Our studies show that the 11b treatment effects occur at lower concentrations than similar effects associated with resveratrol treatments and that microtubules may be the primary target for the observed effects of 11b. These studies suggest that 11b should be further examined as a potentially potent clinical chemotherapeutic agent for treating pancreatic and breast cancer patients.     

A novel class of small functional peptides that bind and inhibit human alpha-thrombin isolated by mRNA display

Here we report the in vitro selection of novel small peptide motifs that bind to human alpha-thrombin. We have applied mRNA display to select for thrombin binding peptides from an unbiased library of 1.2 x 10(11) different 35-mer peptides, each containing a random sequence of 15 amino acids. Two clones showed binding affinities ranging from 166 to 520 nM. A conserved motif of four amino acids, DPGR, was identified. Clot formation of human plasma is inhibited by the selected clones, and they downregulate the thrombin-mediated activation of protein C. The identified peptide motifs do not share primary sequence similarities to any of the known natural thrombin binding motifs. As new inhibitors for human thrombin open interesting possibilities in thrombosis research, our newly identified peptides may provide further insights into this field of investigation and may be possible candidates for the development of new anti-thrombotic agents.     

Involvement of human small fragment nuclease in the resistance of human cells to UV-C-induced cell death

Human small fragment nuclease (Sfn) is one of the cellular proteins that were reported to degrade small, single-stranded DNA and RNA. However, the biological role of Sfn in cellular response to various stressors such as UV-C (mainly 254 nm wavelength ultraviolet ray) remains unclear. We have examined whether modulation of human SFN gene expression affects cell survival capacity against UV-C-induced cell death, analyzing colony survival ability in UV-C-sensitive human RSa cells treated with short double-stranded RNA (siRNA) specific for SFN messenger RNA (mRNA). The expression levels of SFN mRNA in the siRNA-treated RSa cells decreased to about 15% compared with those in the control siRNA-treated cells. The siRNA-treated RSa cells showed lower colony survival and higher activity of caspase-3 after UV-C irradiation than the control siRNA-treated RSa cells. Furthermore, the removal capacity of cyclobutane pyrimidine dimers (CPD) in the siRNA-treated RSa cells decreased compared with the control siRNA-treated RSa cells. There was no difference in the colony survival and CPD removal capacity after UV-C irradiation between the control siRNA-treated RSa cells and mock-treated RSa cells. These results suggest that SFN expression is involved in resistance of RSa cells to UV-C-induced cell death through the roles it plays in the DNA repair process.     

Inhibition of human placenta aldose reductase by tannic acid

Tannic acid was found to be a highly potent inhibitor of human placenta aldose reductase. The most potent inhibitory component of the tannic acid was isolated and identified as penta-O-galloyl-beta-D-glucose, which showed an IC50 value of 70 nM. The inhibition by the gallotannin was reversible and of mixed type with respect to DL-glyceraldehyde as the varied substrate.     

Dedifferentiation of lineage-committed cells by a small molecule

Combinatorial libraries were screened for molecules that induce mouse myogenic lineage committed cells to dedifferentiate in vitro. A 2,6-disubstituted purine, reversine, was discovered that induces lineage reversal of C2C12 cells to become multipotent progenitor cells which can redifferentiate into osteoblasts and adipocytes. This and other such molecules are likely to provide new insights into the molecular mechanisms that control cellular dedifferentiation and may ultimately be useful to in vivo stem cell biology and therapy.     

Quantum phenomena in small semiconductor structures and devices

The ability to artificially structure new semiconductor materials on an atomic scale, using advanced crystal growth methods such as molecular beam epitaxy and metal organic chemical vapor deposition, has led recently to the observation of new physical phenomena as well as the creation of entirely new classes of devices based on band gap and wave function engineering. In these lectures an elementary introduction is given to the quantum aspects of these new structures.     

Isomeric structures and structural transformations in small clusters

The temperature dependence of energies of the isomers of a seven-particle system is studied with a view toward understanding ergodicity problems in Monte Carlo simulations. It is found that the phase space of particles in a cluster is not ergodic at lower temperatures.     

Inhibition of the nicotinamide adenine dinucleotide-oxidoreductase reaction by herbicides and fungicides of various structures

The effect of herbicides (basagran, zenkor, kusagard, roundup, setoxidim, and lontrel and lontrel complexes with some doubly charged metal ions) and fungicides (tachigaren and tilt) on the activity of nicotinamide adenine dinucleotide (NADH)-oxidoreductase from the methylotroph Methylococcus capsulatus (strain M) was studied. All the herbicides and fungicides inhibit the enzyme, differing in the degree and type of inhibition. The inhibition constants K _i for these compounds and for lontrel complexes were determined. A correlation between the K _i values and the complexation constants of these pesticides with NADH was established. The studied compounds are toxic. __________ Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 1284–1289, May, 2005.     

General principles governing structures of small clusters

General rules which govern electronic and geometric structures of small clusters are formulated, and their validity is documented with the results of the MRD - CI investigations for Li _n , BeLi _k , Be _l (n=2?14,k=2?6,l=2?13) as well as on IIa and IVa tetramers. The MRD - CI results are compared with investigations performed with other methods.     

Quantitative measurement of mRNA cap 0 and cap 1 structures by high-performance liquid chromatography

Viral and eukaryotic mRNA molecules have a unique 5'-end. The 5'-terminus consists of m7G(5')ppp(5')N'(m)pN'(m), which is termed a "cap" structure. The study of these cap structures has led to the development of many methods of identification and analysis. Many of the methods have been time-consuming or have not been able to distinguish between the different caps, and they are quantifiable only by employing radiolabels. This paper presents the use of reversed-phase high-performance liquid chromatography as a rapid and efficient tool for the separation, identification and quantitation of caps. An ion-exchange enrichment procedure was also developed for the isolation of cap 0 and cap 1 structures from unfractionated RNAs. The recoveries of different caps ranged from 83 to 99%, with a relative standard deviation range of 1.3-4.4%. In this method, caps were released from commercially obtained rabbit globin mRNA by nuclease P1 digestion. The products of digestion were treated with alkaline phosphatase and separated on an octadecylsilyl column using stepwise or gradient elution. Cap structures and any internal modified nucleosides were identified by their retention times and UV spectra relative to reference compounds. The amount of each cap 0 or cap 1 structure was determined by its UV absorbance relative to a known quantity of reference compound. This method allows the quantitation of 0.2 nmol or more of cap 0 and cap 1 structures. Total UV spectra can be obtained for 0.5 nmol or more of cap. This methodology permits investigations on viral and eukaryotic mRNA cap biosynthesis and turnover during viral transformation, differentiation, cap synthesis in the cell cycle, etc.     

Cellular delivery of dinucleotides by conjugation with small molecules: targeting translation initiation for anticancer applications

Targeting cap-dependent translation initiation is one of the experimental approaches that could lead to the development of novel anti-cancer therapies. Synthetic dinucleoside 5′,5′-triphosphates cap analogs are potent antagonists of eukaryotic translation initiation factor 4E (eIF4E) in vitro and could counteract elevated levels of eIF4E in cancer cells; however, transformation of these compounds into therapeutic agents remains challenging – they do not easily penetrate into cells and are susceptible to enzymatic cleavage. Here, we tested the potential of several small molecule ligands – folic acid, biotin, glucose, and cholesterol – to deliver both hydrolyzable and cleavage-resistant cap analogs into cells. A broad structure–activity relationship (SAR) study using model fluorescent probes and cap–ligand conjugates showed that cholesterol greatly facilitates uptake of cap analogs without disturbing the interactions with eIF4E. The most potent cholesterol conjugate identified showed apoptosis-mediated cytotoxicity towards cancer cells.

Ligand assisted cellular delivery of negatively charged dinucleotides, which are potential antagonists of the protooncogenic protein eIF4E.     

Inhibition of heat-induced aggregation of a beta-lactoglobulin-stabilized emulsion by very small additions of casein

Heat stability has been studied in model systems of oil-in-water emulsions (3 wt.% total protein, 45 vol.% n-tetradecane, pH 6.8, ionic strength 30-50 mM) with pure beta-lactoglobulin (beta-lg) as the main emulsifier. The effect of small additions of sodium caseinate, beta-casein or alpha s1-casein prior to emulsion preparation has been investigated. Samples heated for 3 min at 90 degrees C were monitored with respect to changes in viscosity and particle-size distribution. As expected, the pure beta-lg-stabilized emulsions were susceptible to heat-induced changes. But the replacement of just 1% of the beta-lg by sodium caseinate (0.03 wt.% caseinate in the total emulsion) led to complete elimination of any heat-induced viscosity or particle size increase. These findings show that a very small proportion of casein can inhibit the susceptibility of a beta-lg-based emulsion to heat-induced destabilization. The magnitude of the effect is dependent on the type of casein, with the order of effectiveness being beta-casein>sodium caseinate>alpha s1-casein. This work has potential implications for the development of milk protein-stabilized emulsions of improved shelf life.     

Inhibition of gamma ray-induced apoptosis by stimulatory heterotrimeric GTP binding protein involves Bcl-xL down-regulation in SH-SY5Y human neuroblastoma cells

Heterotrimeric GTP-binding proteins (G proteins) transduce extracellular signals into intracellular signals by activating effector molecules including adenylate cyclases that catalyze cAMP formation, and thus regulate various cellular responses such as metabolism, proliferation, and apoptosis. cAMP signaling pathways have been reported to protect cells from ionizing radiation-induced apoptosis, but however, the protective mechanism is not clear. Therefore, this study aimed to investigate the signaling molecules and the mechanism mediating the anti-apoptotic action of cAMP signaling system in radiation-induced apoptosis. Stable expression of a constitutively active mutant of Gas (GalphasQL) protected gamma ray-induced apoptosis which was assessed by analysis of the cleavages of PARP, caspase-9, and caspase-3 and cytochrome C release in SH-SY5Y human neuroblastoma cells. GasQL repressed the gamma ray-induced down-regulation of Bcl-xL protein, but transfection of Bcl-xL siRNA increased the gamma ray-induced apoptosis and abolished the anti-apoptotic effect of GasQL. GasQL decreased the degradation rate of Bcl-xL protein, and it also restrained the decrease in Bcl-xL mRNA by increasing the stability following ionizing irradiation. Furthermore, prostaglandin E2 that activates Gas was found to protect gamma ray-induced apoptosis, and the protective effect was abolished by treatment with prostanoid receptor antagonist specific to EP2/4R subtype. Moreover, specific agonists for adenosine A1 receptor that inhibits cAMP signaling pathway augmented gamma ray-induced apoptosis. From this study, it is concluded that Galphas-cAMP signaling system can protect SH-SY5Y cells from gamma ray-induced apoptosis partly by restraining down-regulation of Bcl-xL expression, suggesting that radiation-induced apoptosis can be modulated by GPCR ligands to improve the efficiency of radiation therapy.     

Inhibition of anti-hapten antibody plaque-forming cells by a chemically reactive hapten

The ability of the chemically reactive hapten 2–426̄-trinitrobezene sulp acid (TNBSA) to inhibit anti-TNP IgM antibody plaque-forming cells (APFC) was investigated. TNBSA at a concentration of 1 mg (3 × 10⁻³M) to 0.3 mg (10⁻³) completely inhibited IgM anti-TNP APFC after a 10-min incubation period at 37°C. This inhibition was specific and did not alter the antifluorescein IgM antibody response.After a 24-h culture period in tissue culture medium without antigen, the non-dividing APFC remained inhibited, whereas the dividing APFC escaped this inhibition.     

Identification of phospholipid structures in human blood by direct-injection quadrupole-linear ion-trap mass spectrometry

Direct-injection electrospray ionization mass spectrometry in combination with information-dependent data acquisition (IDA), using a triple-quadrupole/linear ion trap combination, allows high-throughput qualitative analysis of complex phospholipid species from child whole blood. In the IDA experiments, scans to detect specific head groups (precursor ion or neutral loss scans) were used as survey scans to detect phospholipid classes. An enhanced resolution scan was then used to confirm the mass assignments, and the enhanced product ion scan was implemented as a dependent scan to determine the composition of each phospholipid class. These survey and dependent scans were performed sequentially and repeated for the entire duration of analysis, thus providing the maximum information from a single injection. In this way, 50 different phospholipids belonging to the phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, phosphatidylcholine and sphingomyelin classes were identified in child whole blood.