More than just scanning: the importance of cap-independent mRNA translation initiation for cellular stress response and cancer

The scanning model for eukaryotic mRNA translation initiation states that the small ribosomal subunit, along with initiation factors, binds at the cap structure at the 5′ end of the mRNA and scans the 5′ untranslated region (5′UTR) until an initiation codon is found. However, under conditions that impair canonical cap-dependent translation, the synthesis of some proteins is kept by alternative mechanisms that are required for cell survival and stress recovery. Alternative modes of translation initiation include cap- and/or scanning-independent mechanisms of ribosomal recruitment. In most cap-independent translation initiation events there is a direct recruitment of the 40S ribosome into a position upstream, or directly at, the initiation codon via a specific internal ribosome entry site (IRES) element in the 5′UTR. Yet, in some cellular mRNAs, a different translation initiation mechanism that is neither cap- nor IRES-dependent seems to occur through a special RNA structure called cap-independent translational enhancer (CITE). Recent evidence uncovered a distinct mechanism through which mRNAs containing N ⁶-methyladenosine (m⁶A) residues in their 5′UTR directly bind eukaryotic initiation factor 3 (eIF3) and the 40S ribosomal subunit in order to initiate translation in the absence of the cap-binding proteins. This review focuses on the important role of cap-independent translation mechanisms in human cells and how these alternative mechanisms can either act individually or cooperate with other cis-acting RNA regulons to orchestrate specific translational responses triggered upon several cellular stress states, and diseases such as cancer. Elucidation of these non-canonical mechanisms reveals the complexity of translational control and points out their potential as prospective novel therapeutic targets.     

Antimicrobial and antiviral activity of xylosyl-methylthio-adenosine, a naturally occurring analogue of methylthio-adenosine from Doris verrucosa.

Xylosyl-methylthio-adenosine, a naturally occurring analogue of 5'-deoxy-5'-methylthio-adenosine, has been postulated to play a protective role during egg development in the mollusc Doris verrucosa. However, in vitro tests showed that this analogue is devoid of activity against fungi, bacteria and viruses.     

The effect of a bradykinin antagonist on vasodilator responses with particular reference to the submandibular gland of the cat

Summary A bradykinin analogue, D-Arg[Hyp³, Thi^{5, 8}, D-Phe⁷]-Bk, antagonized the vasodilator effect of bradykinin injected close-arterially in the submandibular salivary gland of the cat, without affecting that due to acetylcholine or nerve stimulation. The same analogue also antagonized the hypotensive response to bradykinin injected intravenously in cats and rabbits. We conclude that functional hyperaemia in the submandibular gland of the cat is not due to the release of bradykinin by salivary kallikrein.     

The morals of model-making

I address questions about values in model-making in engineering, specifically: Might the role of values be attributable solely to interests involved in specifying and using the model? Selected examples illustrate the surprisingly wide variety of things one must take into account in the model-making itself. The notions of system (as used in engineering thermodynamics), and physically similar systems (as used in the physical sciences) are important and powerful in determining what is relevant to an engineering model. Another example (windfarms) illustrates how an idea to completely re-characterize, or reframe, an engineering problem arose during model-making.I employ a qualitative analogue of the notion of physically similar systems. Historical cases can thus be drawn upon; I illustrate with a comparison between a geoengineering proposal to inject, or spray, sulfate aerosols, and two different historical cases involving the spraying of DDT (fire ant eradication; malaria eradication). The current geoengineering proposal is seen to be like the disastrous and counterproductive case, and unlike the successful case, of the spraying of DDT. I conclude by explaining my view that model-making in science is analogous to moral perception in action, drawing on a view in moral theory that has come to be called moral particularism.     

microRNA-122 target sites in the hepatitis C virus RNA NS5B coding region and 3′ untranslated region: function in replication and influence of RNA secondary structure

We have analyzed the binding of the liver-specific microRNA-122 (miR-122) to three conserved target sites of hepatitis C virus (HCV) RNA, two in the non-structural protein 5B (NS5B) coding region and one in the 3′ untranslated region (3′UTR). miR-122 binding efficiency strongly depends on target site accessibility under conditions when the range of flanking sequences available for the formation of local RNA secondary structures changes. Our results indicate that the particular sequence feature that contributes most to the correlation between target site accessibility and binding strength varies between different target sites. This suggests that the dynamics of miRNA/Ago2 binding not only depends on the target site itself but also on flanking sequence context to a considerable extent, in particular in a small viral genome in which strong selection constraints act on coding sequence and overlapping cis-signals and model the accessibility of cis-signals. In full-length genomes, single and combination mutations in the miR-122 target sites reveal that site 5B.2 is positively involved in regulating overall genome replication efficiency, whereas mutation of site 5B.3 showed a weaker effect. Mutation of the 3′UTR site and double or triple mutants showed no significant overall effect on genome replication, whereas in a translation reporter RNA, the 3′UTR target site inhibits translation directed by the HCV 5′UTR. Thus, the miR-122 target sites in the 3′-region of the HCV genome are involved in a complex interplay in regulating different steps of the HCV replication cycle.     

Endonuclease V: an unusual enzyme for repair of DNA deamination

Endonuclease V (endo V) was first discovered as the fifth endonuclease in Escherichia coli in 1977 and later rediscovered as a deoxyinosine 3′ endonuclease. Decades of biochemical and genetic investigations have accumulated rich information on its role as a DNA repair enzyme for the removal of deaminated bases. Structural and biochemical analyses have offered invaluable insights on its recognition capacity, catalytic mechanism, and multitude of enzymatic activities. The roles of endo V in genome maintenance have been validated in both prokaryotic and eukaryotic organisms. The ubiquitous nature of endo V in the three domains of life: Bacteria, Archaea, and Eukaryotes, indicates its existence in the early evolutionary stage of cellular life. The application of endo V in mutation detection and DNA manipulation underscores its value beyond cellular DNA repair. This review is intended to provide a comprehensive account of the historic aspects, biochemical, structural biological, genetic and biotechnological studies of this unusual DNA repair enzyme.     

Differential effects of calcium channel blockers on the responses of the rat vas deferens to intramural nerve stimulation and exogenous drugs

Summary The calcium channel blockers, nifedipine and verapamil, have separate effects on the phases of nerve-induced twitches which are not reflected by their actions on the responses to exogenous NA, ATP and the stable ATP analogue, ,-mATP. This implies that different calcium channels are used according to the manner of stimulation.     

The action of the cholecystokinin-A receptor antagonist,devazepide, on the digestive system of the chicken

The influence of the cholecystokinin (CCK)-A receptor antagonist, devazepide (DVZ), on the chicken digestive tract was investigated. The passage of food from the crops of birds treated with DVZ was not significantly different from that of the control. DVZ treatment did not inhibit the biliary flow stimulated by the CCK analogue, caerulein. Dispersed chicken pancreatic acini stimulated with CCK were treated with various concentrations of DVZ. At 10^–5 M, DVZ completely inhibited amylase release; this concentration was much higher than those reported to have similar effects in mammals. The results suggest that the action DVZ as a CCK antagonist in the chicken is very weak.     

Synthesis of O1.5-(beta-D-galactopyranosyl) [DMet2, Hyp5] enkephalin amide, a new highly potent analgesic enkephalin-related glycosyl peptide

A new series of O-glycosyl enkephalins has been prepared, following a convergent strategy, with high chemical yields. The galactosyl analogue, O1.5-(beta-D-galactopyranosyl) [DMet2, Hyp5] enkephalin amide proved to be one of the most potent in vivo opioid agonists synthesized up to now.     

Effect of administration of synthetic ecdysone on the moulting ofPalamnaeus bengalensis

Summary Synthetic analogue of ecdysone, 3, 14-dihydroxy-5-cholest-7-en-6-one did not bring the scorpionPalamnaeus bengalensis to moult. It also failed completely in stimulating the scorption to produce any change related to moulting.Acknowledgment. Author is grateful to Dr Suresh C. Shrivastava for providing research facilities, Dr S.P. Tewarson for encouragement and S.C.S.T. (U.P.) for funds. Present address: Department of Zoology, Lucknow Christian College, Lucknow-226001.     

Regulation of class V myosin

Class V myosin (myosin-5) is a molecular motor that functions as an organelle transporter. The activation of myosin-5′s motor function has long been known to be associated with a transition from the folded conformation in the off-state to the extended conformation in the on-state, but only recently have we begun to understand the underlying mechanism. The globular tail domain (GTD) of myosin-5 has been identified as the inhibitory domain and has recently been shown to function as a dimer in regulating the motor function. The folded off-state of myosin-5 is stabilized by multiple intramolecular interactions, including head–GTD interactions, GTD–GTD interactions, and interactions between the GTD and the C-terminus of the first coiled-coil segment. Any cellular factor that affects these intramolecular interactions and thus the stability of the folded conformation of myosin-5 would be expected to regulate myosin-5 motor function. Both the adaptor proteins of myosin-5 and Ca²⁺ are potential regulators of myosin-5 motor function, because they can destabilize its folded conformation. A combination of these regulators provides a versatile scheme in regulating myosin-5 motor function in the cell.     

Synthesis ofO 1.5-(β-D-galactopyranosyl) [DMet2, Hyp5] enkephalin amide,a new highly potent analgesic enkephalin-related glycosyl peptide

Summary A new series of O-glycosyl enkephalins has been prepared, following a convergent strategy, with high chemical yields. The galactosyl analogue,O ^1.5-(-D-galactopyranosyl) [DMet², Hyp⁵] enkephalin amide proved to be one of the most potent in vivo opioid agonists synthesized up to now.     

A comparison of pyridoxal 5′-phosphate dependent decarboxylase and transaminase enzymes at a molecular level

Pyridoxal 5′-phosphate is a coenzyme for a number of enzymes which catalyse reactions at C^α of amino acid substrates including transaminases, decarboxylases and serine hydroxymethyltransferase. Using the X-ray coordinates for a transaminase, aspartate aminotransferase, and the results of stereochemical and mechanistic studies for decarboxylases and serine hydroxymethyltransferase, an active-site structure for the decarboxylase group is constructed. The structure of the active-site is further refined through active-site pyridoxyllysine peptide sequence comparison and a 3-D catalytic mechanism for the L-α-amino acid decarboxylases is proposed. The chemistry of serine hydroxymethyltransferase is re-examined in the light of the proposed decarboxylase mechanism.     

The cyclin-dependent kinase family in the social amoebozoan Dictyostelium discoideum

Cyclin-dependent kinases (Cdk) are a family of serine/threonine protein kinases that regulate eukaryotic cell cycle progression. Their ability to modulate the cell cycle has made them an attractive target for anti-cancer therapies. Cdk protein function has been studied in a variety of Eukaryotes ranging from yeast to humans. In the social amoebozoan Dictyostelium discoideum, several homologues of mammalian Cdks have been identified and characterized. The life cycle of this model organism is comprised of a feeding stage where single cells grow and divide mitotically as they feed on their bacterial food source and a multicellular developmental stage that is induced by starvation. Thus it is a valuable system for studying a variety of cellular and developmental processes. In this review I summarize the current knowledge of the Cdk protein family in Dictyostelium by highlighting the research efforts focused on the characterization of Cdk1, Cdk5, and Cdk8 in this model Eukaryote. Accumulated evidence indicates that each protein performs distinct functions during the Dictyostelium life cycle with Cdk1 being required for growth and Cdk5 and Cdk8 being required for processes that occur during development. Recent studies have shown that Dictyostelium Cdk5 shares attributes with mammalian Cdk5 and that the mammalian Cdk inhibitor roscovitine can be used to inhibit Cdk5 activity in Dictyostelium. Together, these results show that Dictyostelium can be used as a model system for studying Cdk protein function.