Interaction of the HIV-1 frameshift signal with the ribosome

Ribosomal frameshifting on viral RNAs relies on the mechanical properties of structural elements, often pseudoknots and more rarely stem-loops, that are unfolded by the ribosome during translation. In human immunodeficiency virus (HIV)-1 type B a long hairpin containing a three-nucleotide bulge is responsible for efficient frameshifting. This three-nucleotide bulge separates the hairpin in two domains: an unstable lower stem followed by a GC-rich upper stem. Toeprinting and chemical probing assays suggest that a hairpin-like structure is retained when ribosomes, initially bound at the slippery sequence, were allowed multiple EF-G catalyzed translocation cycles. However, while the upper stem remains intact the lower stem readily melts. After the first, and single step of translocation of deacylated tRNA to the 30 S P site, movement of the mRNA stem-loop in the 5′ direction is halted, which is consistent with the notion that the downstream secondary structure resists unfolding. Mechanical stretching of the hairpin using optical tweezers only allows clear identification of unfolding of the upper stem at a force of 12.8 ± 1.0 pN. This suggests that the lower stem is unstable and may indeed readily unfold in the presence of a translocating ribosome.     

Overcoming the anaerobic hurdle in phenotypic microarrays: generation and visualization of growth curve data for Desulfovibrio vulgaris Hildenborough

Growing anaerobic microorganisms in phenotypic microarrays (PM) and 96-well microtiter plates is an emerging technology that allows high throughput survey of the growth and physiology and/or phenotype of cultivable microorganisms. For non-model bacteria, a method for phenotypic analysis is invaluable, not only to serve as a starting point for further evaluation, but also to provide a broad understanding of the physiology of an uncharacterized wild-type organism or the physiology/phenotype of a newly created mutant of that organism. Given recent advances in genetic characterization and targeted mutations to elucidate genetic networks and metabolic pathways, high-throughput methods for determining phenotypic differences are essential. Here we outline challenges presented in studying the physiology and phenotype of a sulfate-reducing anaerobic delta proteobacterium, Desulfovibrio vulgaris Hildenborough. Modifications of the commercially available OmniLog system (Hayward, CA) for experimental setup, and configuration, as well as considerations in PM data analysis are presented. Also highlighted here is data viewing software that enables users to view and compare multiple PM data sets. The PM method promises to be a valuable strategy in our systems biology approach to D. vulgaris studies and is readily applicable to other anaerobic and aerobic bacteria.     

A new stage 3 millennial climatic variability record from a SW France speleothem

We present a new high resolution speleothem stable isotope record from the Villars Cave (SW-France) that covers part of marine isotope stage (MIS) 3. The Vil14 stalagmite grew between ~ 52 and 29 ka. The δ¹³C profile is used as a palaeoclimate proxy and clearly shows the interstadial substages 13, 12 and 11. The new results complement and corroborate previously published stalagmite records Vil9 and Vil27 from the same site. The Vil14 stalagmite chronology is based on 12 Th-U dating by MC-ICP-MS and 3 by TIMS. A correction for detrital contamination was done using the ²³⁰Th/²³²Th activity ratio measured on clay collected in Villars Cave. The Vil14 results reveal that the onset of Dansgaard–Oeschger (DO) events 13 and 12 occurred at ~ 49.8 ka and ~ 47.8 ka, respectively. Within uncertainties, this is coherent with the latest NorthGRIP time scale (GICC05-60 ka) and with speleothem records from Central Alps. Our data show an abrupt δ¹³C increase at the end of DO events 14 to 12 which coincides with a petrographical discontinuity probably due to a rapid cooling. As observed for Vil9 and Vil27, Vil14 growth significantly slowed down after ~ 42 ka and finally stopped ~ 29 ka ago where the δ¹³C increase suggests a strong climate deterioration that coincides with both North Atlantic sea level and sea surface temperature drop.     

The nature of Staphylococcus aureus MurA and MurZ and approaches for detection of peptidoglycan biosynthesis inhibitors

Staphylococcus aureus and a number of other Gram-positive organisms harbour two genes ( murA and murZ ) encoding UDP- N -acetylglucosamine enolpyruvyl transferase activity for catalysing the first committed step of peptidoglycan biosynthesis. We independently inactivated murA and murZ in S. aureus and established that either can sustain viability. Purification and characterization of the MurA and MurZ enzymes indicated that they are biochemically similar in vitro , consistent with similar overall structures predicted for the isozymes by molecular modelling. Nevertheless, MurA appears to be the primary enzyme utilized in the staphylococcal cell. Accordingly, murA expression was approximately five times greater than murZ expression during exponential growth, and the peptidoglycan content of S. aureus was reduced by approximately 25% following inactivation of murA , but remained almost unchanged following inactivation of murZ . Despite low level expression during normal growth, murZ expression was strongly induced (up to sixfold) following exposure to inhibitors of peptidoglycan biosynthesis, which was not observed for murA . Strains generated in this study were validated as potential tools for identifying novel anti-staphylococcal agents targeting peptidoglycan biosynthesis using known inhibitors of the pathway.     

3D strain map of axially loaded mouse tibia: a numerical analysis validated by experimental measurements

A combined experimental/numerical study was performed to calculate the 3D octahedral shear strain map in a mouse tibia loaded axially. This study is motivated by the fact that the bone remodelling analysis, in this in vivo mouse model should be performed at the zone of highest mechanical stimulus to maximise the measured effects. Accordingly, it is proposed that quantification of bone remodelling should be performed at the tibial crest and at the distal diaphysis. The numerical model could also be used to furnish a more subtle analysis as a precise correlation between local strain and local biological response can be obtained with the experimentally validated numerical model.     

Interleukin-33 Is Biologically Active Independently of Caspase-1 Cleavage

The new interleukin (IL)-1 family cytokine IL-33 is synthesized as a 30-kDa precursor. Like pro-IL-1β, human pro-IL-33 was reported to be cleaved by caspase-1 to generate an 18-kDa fragment, which is sufficient to activate signaling by the IL-33 receptor T1/ST2. However, the proposed caspase-1 cleavage site is poorly conserved between species. In addition, it is not clear whether caspase-1 cleavage of pro-IL-33 occurs in vivo and whether, as for IL-1β, this cleavage is a prerequisite for IL-33 secretion and bioactivity. In this study, we further investigated caspase-1 cleavage of mouse and human pro-IL-33 and assessed the potential bioactivity of the IL-33 precursor. We observed the generation of a 20-kDa IL-33 fragment in cell lysates, which was enhanced by incubation with caspase-1. However, in vitro assays of mouse and human pro-IL-33 indicated that IL-33 is not a direct substrate for this enzyme. Consistently, caspase-1 activation in THP-1 cells induced cleavage of pro-IL-1β but not of pro-IL-33, and activated THP-1 cells released full-length pro-IL-33 into culture supernatants. Finally, addition of full-length pro-IL-33 induced T1/ST2-dependent IL-6 secretion in mast cells. However, we observed in situ processing of pro-IL-33 in mast cell cultures, and it remains to be determined whether full-length pro-IL-33 itself indeed represents the bioactive species. In conclusion, our data indicate that pro-IL-33 is not a direct substrate for caspase-1. In addition, our results clearly show that caspase-1 cleavage is not required for pro-IL-33 secretion and bioactivity, highlighting major differences between IL-1β and IL-33.Interleukin (IL)² -33, the most recently described cytokine of the IL-1 family, is synthesized as a 30-kDa precursor. Human pro-IL-33, like pro-IL-1β, was reported to be cleaved by caspase-1 in vitro to generate an 18-kDa fragment, termed mature IL-33, which is sufficient to activate signaling by the IL-33 receptor T1/ST2 (1).Caspase-1 is an endoproteinase that specifically cleaves Asp-Xaa bonds, where Xaa typically refers to a small, often hydrophobic residue (2–4). Caspase-1 activity absolutely requires the presence of an Asp residue at position −1 of the cleavage site. Consistently, replacement of Asp¹¹⁶ by other amino acids, such as Ala, was previously demonstrated to prevent caspase-1 cleavage of pro-IL-1β (2). Recombinant (r) mature IL-33 starts at Ser¹¹² for human (h) IL-33 and at Ser¹⁰⁹ for mouse (m) IL-33, neither of which corresponds exactly to the position of a potential caspase-1 cleavage site. Indeed, the N-terminal moiety of human pro-IL-33 sequence contains a single Asp at position 110, and the N-terminal portion of mouse pro-IL-33 contains an Asp at positions 88 and 106. In fact, the region located between amino acids 80 and 110 of pro-IL-33 is rather poorly conserved between species (5). In particular, no Asp residues can be consistently found at an identical position across species to hint at the presence of a conserved caspase-1 cleavage site. So far, caspase-1 cleavage of pro-IL-33 has not been investigated in any species other than human.Expression of endogenous IL-33 has been described most extensively in endothelial cells, where essentially nuclear, full-length 30-kDa pro-IL-33 is detected (5–7). To date, only two studies have examined potential effects of caspase-1 activation on the processing and secretion of pro-IL-33 in living cells. In one study, stimulation of murine glial cultures with caspase-1 activators induced secretion of bioactive IL-33 into culture supernatants, but the size of the secreted protein was not assessed (8). It is thus not clear whether caspase-1 cleavage of pro-IL-33 occurs in mouse cells. In a second study, Western blot analysis revealed the presence of a 32-kDa protein and minor 17 and 20 kDa bands reacting with anti-IL-33 antibodies in the supernatants of THP-1 cells upon caspase-1 activation, suggesting secretion of full-length pro-IL-33 and of two potential cleavage products (9). Although this last observation suggests that some pro-IL-33 may be secreted, it not known to what extent IL-33 secretion is dependent on caspase-1 cleavage. Finally, so far all studies reporting T1/ST2-mediated effects of IL-33 were performed using the recombinant mature form of IL-33, whereas potential biological activity of the full-length precursor form has not been tested. It thus remains to be shown whether, as for IL-1β, caspase-1 cleavage is indeed required for IL-33 bioactivity. In the present study, we thus further investigated caspase-1 cleavage of mouse and human pro-IL-33 in vitro and in cultured cells and assessed the potential bioactivity of the IL-33 precursor.     

ADAM function in embryogenesis

Cleavage of proteins inserted into the plasma membrane (shedding) is an essential process controlling many biological functions including cell signaling, cell adhesion and migration as well as proliferation and differentiation. ADAM surface metalloproteases have been shown to play an essential role in these processes. Gene inactivation during embryonic development have provided evidence of the central role of ADAM proteins in nematodes, flies, frogs, birds and mammals. The relative contribution of four subfamilies of ADAM proteins to developmental processes is the focus of this review.