Size matters: a view of selenocysteine incorporation from the ribosome

This review focuses on the known factors required for selenocysteine (Sec) incorporation in eukaryotes and highlights recent findings that have compelled us to propose a new model for the mechanism of Sec incorporation. In light of this data we also review the controversial aspects of the previous modelspecifically regarding the proposed interaction between SBP2 and eEFSec. In addition, the relevance of two recently discovered factors in the recoding of Sec are reviewed. The role of the ribosome in this process is emphasized along with a detailed analysis of kinkturn structures present in the ribosome and the L7Ae RNA-binding motif present in SBP2 and other proteins. Received 2 September 2005; received after revision 28 September 2005; accepted 12 October 2005     

Synonymous codons,ribosome speed,and eukaryotic gene expression regulation

Quantitative control of gene expression occurs at multiple levels, including the level of translation. Within the overall process of translation, most identified regulatory processes impinge on the initiation phase. However, recent studies have revealed that the elongation phase can also regulate translation if elongation and initiation occur with specific, not mutually compatible rate parameters. Translation elongation then limits the overall amount of protein that can be made from an mRNA. Several recently discovered control mechanisms of biological pathways are based on such elongation control. Here, we review the molecular mechanisms that determine ribosome speed in eukaryotic organisms, and discuss under which conditions ribosome speed can become the controlling parameter of gene expression levels.     

A creature with a hundred waggly tails: intrinsically disordered proteins in the ribosome

Intrinsic disorder (i.e., lack of a unique 3-D structure) is a common phenomenon, and many biologically active proteins are disordered as a whole, or contain long disordered regions. These intrinsically disordered proteins/regions constitute a significant part of all proteomes, and their functional repertoire is complementary to functions of ordered proteins. In fact, intrinsic disorder represents an important driving force for many specific functions. An illustrative example of such disorder-centric functional class is RNA-binding proteins. In this study, we present the results of comprehensive bioinformatics analyses of the abundance and roles of intrinsic disorder in 3,411 ribosomal proteins from 32 species. We show that many ribosomal proteins are intrinsically disordered or hybrid proteins that contain ordered and disordered domains. Predicted globular domains of many ribosomal proteins contain noticeable regions of intrinsic disorder. We also show that disorder in ribosomal proteins has different characteristics compared to other proteins that interact with RNA and DNA including overall abundance, evolutionary conservation, and involvement in protein–protein interactions. Furthermore, intrinsic disorder is not only abundant in the ribosomal proteins, but we demonstrate that it is absolutely necessary for their various functions.     

The E-site story: the importance of maintaining two tRNAs on the ribosome during protein synthesis

In the sixties James Watson suggested a twosite model for the ribosome comprising the P site for the peptidyl transfer RNA (tRNA) before peptide-bond formation and the A site, where decoding takes place according to the codon exposed there. In the eighties a third tRNA binding site was detected, the E site, which was specific for deacylated tRNA and turned out to be a universal feature of ribosomes. However, despite having three tRNA binding sites, only two tRNAs occupy the ribosome at a time during protein synthesis: at the A and P sites before translocation (PRE state) and at the P and E sites after translocation (POST state). The importance of having two tRNAs in the POST state has been revealed during the last 25 years, showing that the E site contributes two fundamental features: (i) the fact that incorporation of a wrong amino acid is not harmful for the cell (only 1 in about 400 misincorporations destroys the function of a protein) stems from the presence of an E-tRNA; (ii) maintenance of the reading frame is one of the most remarkable achievements of the ribosome, essential for faithful translation of the genetic information. The presence of the POST state E-tRNA prevents loss of the reading frame. Received 14 March 2006; received after revision 8 June 2006; accepted 4 August 2006     

Evidence for a novel cytoplasmic processing event in ribosome maturation in the sea urchin Paracentrotus lividus

In this paper we demonstrate the existence of a cytoplasmic processing step, never before described, involving both the pre-ribosomal subunits in the sea urchin Paracentrotus lividus. Northern-blot hybridization, primer extension, S1 mapping experiments and in situ hybridizations allowed us to demonstrate that cytoplasmic processed particles are successively re-imported into the nucleus where maturation of their RNAs is completed prior to being exported to the cytoplasm. Our findings lead to the proposal of a new model of ribosome maturation and shuttling.     

Inhibition of hepatitis C virus internal ribosome entry site-mediated translation by an RNA targeting the conserved IIIf domain

Hepatitis C virus (HCV) translation initiation depends on an internal ribosome entry site (IRES). We previously identified an RNA molecule (HH363–10) able to bind and cleave the HCV IRES region. This paper characterizes its capacity to interfere with IRES function. Inhibition assays showed that it blocks IRES activity both in vitro and in a human hepatoma cell line. Although nucleotides involved in binding and cleavage reside in separate regions of the inhibitor HH363–10, further analysis demonstrated the strongest effect to be an intrinsic feature of the entire molecule; the abolishment of either of the two activities resulted in a reduction in its function. Probing assays demonstrate that HH363–10 specifically interacts with the conserved IIIf domain of the pseudoknot structure in the IRES, leading to the inhibition of the formation of translationally competent 80S particles. The combination of two inhibitory activities targeting different sequences in a chimeric molecule may be a good strategy to avoid the emergence of resistant viral variants. Received 26 July 2007; received after revision 24 September 2007; accepted 26 September 2007     

A new antisickling agent: In vitro studies of its effect on S/S erthrocytes and on hemoglobin S

Summary 2-{benzoylamino} pyridinium benzoate (BAPB) has exhibited an antisickling effect with homozygous S/S erythrocytes in vitro. This study suggests that BAPB prevents sicklin by inhibiting the gelation of hemoglobin S.Acknowledgments. This research has been partly funded by a Sickle Cell Research grant from the State of Tennessee to Meharry Medical College. We gratefully appreciate the technical assistance of Mr Rudolf Harlan and Mrs Marjorie Deveau of the School of Graduate Studies. We offer our thanks to Dr J. W. Davis, J. D., Coordinator, Sickle Cell Project, Meharry Medical College for constant encouragement.     

A new antisickling agent: in vitro studies of its effect on S/S erythrocytes and on hemoglobin S

2-(benzoylamino) pyridinium benzoate (BAPB) has exhibited an antisickling effect with homozygous S/S erythrocytes in vitro. This study suggests that BAPB prevents sickling by inhibiting the gelation of hemoglobin S.     

The SARS-CoV S glycoprotein

The severe acute respiratory syndrome-coronavirus (SARS-CoV) spike (S) glycoprotein alone can mediate the membrane fusion required for virus entry and cell fusion. It is also a major immunogen and a target for entry inhibitors. Recent rapid advances in our knowledge of the structure and function of this protein have lead to the development of a number of candidate vaccine immunogens and SARS-CoV entry inhibitors.     

Electrophoretic analysis of lactate NAD oxidoreductase in interspecific hybrids between three species of the genus Sphaeroma: S. monodi, S. Rugicauda and S. hookeri]

The electrophoretic analysis of lactate NAD oxydoreductase in interspecific hybrids between three species of genus Sphaeroma (S. monodi, S. rugicauda and S. hookeri hookeri) leads, for each category of hybrids, to a distribution between the two parental enzymatic patterns and, consequently, shows the absence of an isozyme appropriate to these hybrids.     

Production d'anticorps 7 S et 19 S chez des Rats d'âge différent

Summary Antibodies produced following injections of a proteinic antigen emulsified in Freund's adjuvant were studied by the passive hemagglutination test in some lots of WCF rats, varying in age. It is shown by treating sera with mercaptoethanol that older animals produce less 7 S antibodies than younger ones, and that, despite this difference, rats remain able to elaborate seric antibodies at relatively high rates during their senescence period.

---

---

Service du DocteurH. Kaufmann.     

Structure and assembly of the 20S proteasome

The barrel-shaped 20S proteasome is one of the two components of a larger 26S particle, the multicatalytic 2000-kDa protease complex. The proteolytic sites are located in the inner chamber of the 20S particle and are only accessible via narrow entrances. This paper reviews the current knowledge concerning proteasome formation, proteolytic activities, structural aspects and assembly. Eukaryotic proteasomes are made up by four rings each of which contains seven different subunits occurring at fixed positions. While the outer rings contain α-type subunits, the inner ones comprise β-type subunits. The current assembly model for eukaryotic 20S proteasomes is based upon the detection of 13S and 16S intermediates, respectively, in addition to previous findings with archaebacterial and eubacterial proteasome assembly. The available data suggest a cooperative assembly of the α-type and β-type subunits into half proteasome-like complexes followed by dimerization into proteasomes. During or after dimerization of half proteasomes, the β-type subunits are processed. The prosequence of the β-type subunits is essential for the assembly process and prevents protease activity of immature proteasomes.     

The insulin-degrading enzyme is an allosteric modulator of the 20S proteasome and a potential competitor of the 19S

The interaction of insulin-degrading enzyme (IDE) with the main intracellular proteasome assemblies (i.e, 30S, 26S and 20S) was analyzed by enzymatic activity, mass spectrometry and native gel electrophoresis. IDE was mainly detected in association with assemblies with at least one free 20S end and biochemical investigations suggest that IDE competes with the 19S in vitro. IDE directly binds the 20S and affects its proteolytic activities in a bimodal fashion, very similar in human and yeast 20S, inhibiting at (IDE)?≤?30 nM and activating at (IDE)?≥?30 nM. Only an activating effect is observed in a yeast mutant locked in the “open” conformation (i.e., the α-3ΔN 20S), envisaging a possible role of IDE as modulator of the 20S “open”–”closed” allosteric equilibrium. Protein–protein docking in silico proposes that the interaction between IDE and the 20S could involve the C-term helix of the 20S α-3 subunit which regulates the gate opening of the 20S.