The Importance of Marine Research Infrastructures in Capturing Processes and Impacts of Extreme Events

Extreme events have long been underestimated in the extent to which they shape the surface of our planet, our environment, its ecological integrity, and the sustainability of human society. Extreme events are by definition rarely observed, of significant impact and, as a result of their spatiotemporal range, not always easily predicted. Extremes may be short-term catastrophic events such as tsunamis, or long-term evolving events such as those linked to climate change; both modify the environment, producing irreversible changes or regime shifts. Whatever the driver that triggers the extreme event, the damages are often due to a combination of several processes and their impacts can affect large areas with secondary events (domino effect), whose effects in turn may persist well beyond the duration of the trigger event itself. Early studies of extreme events were limited to opportunistic approaches: observations were made within the context of naturally occurring events with high societal impact. Given that climate change is now moving us out of a relatively static climate regime during the development of human civilization, extreme events are now a function of underlying climate shifts overlain by catastrophic processes. Their impacts are often due to synergistic factors, all relevant in understanding process dynamics; therefore, an integrated methodology has become essential to enhance the reliability of new assessments and to develop strategies to mitigate societal impacts. Here we summarize the current state of extreme event monitoring in the marine system, highlighting the advantages of a multidisciplinary approach using Research Infrastructures for providing the temporal and spatial resolution required to monitor Earth processes and enhance assessment of associated impacts.publishedVersio

Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes

Assembly of 30S ribosomes involves the hierarchical addition of ribosomal proteins that progressively stabilize the folded 16S rRNA. Here, we use three-color single molecule FRET to show how combinations of ribosomal proteins uS4, uS17 and bS20 in the 16S 5' domain enable the recruitment of protein bS16, the next protein to join the complex. Analysis of real-time bS16 binding events shows that bS16 binds both native and non-native forms of the rRNA. The native rRNA conformation is increasingly favored after bS16 binds, explaining how bS16 drives later steps of 30S assembly. Chemical footprinting and molecular dynamics simulations show that each ribosomal protein switches the 16S conformation and dampens fluctuations at the interface between rRNA subdomains where bS16 binds. The results suggest that specific protein-induced changes in the rRNA dynamics underlie the hierarchy of 30S assembly and simplify the search for the native ribosome structure

Binding of aminoglycoside antibiotics to helix 69 of 23S rRNA

Aminoglycosides antibiotics negate dissociation and recycling of the bacterial ribosome’s subunits by binding to Helix 69 (H69) of 23S rRNA. The differential binding of various aminoglycosides to the chemically synthesized terminal domains of the Escherichia coli and human H69 has been characterized using spectroscopy, calorimetry and NMR. The unmodified E. coli H69 hairpin exhibited a significantly higher affinity for neomycin B and tobramycin than for paromomycin (Kds = 0.3 ± 0.1, 0.2 ± 0.2 and 5.4 ± 1.1 µM, respectively). The binding of streptomycin was too weak to assess. In contrast to the E. coli H69, the human 28S rRNA H69 had a considerable decrease in affinity for the antibiotics, an important validation of the bacterial target. The three conserved pseudouridine modifications (Ψ1911, Ψ1915, Ψ1917) occurring in the loop of the E. coli H69 affected the dissociation constant, but not the stoichiometry for the binding of paromomycin (Kd = 2.6 ± 0.1 µM). G1906 and G1921, observed by NMR spectrometry, figured predominantly in the aminoglycoside binding to H69. The higher affinity of the E. coli H69 for neomycin B and tobramycin, as compared to paromomycin and streptomycin, indicates differences in the efficacy of the aminoglycosides

pH-dependent structural changes of helix 69 from Escherichia coli 23S ribosomal RNA

Helix 69 in 23S rRNA is a region in the ribosome that participates in a considerable number of RNA–RNA and RNA–protein interactions. Conformational flexibility is essential for such a region to interact and accommodate protein factors at different stages of protein biosynthesis. In this study, pH-dependent structural and stability changes were observed for helix 69 through a variety of spectroscopic techniques, such as circular dichroism spectroscopy, UV melting, and nuclear magnetic resonance spectroscopy. In Escherichia coli 23S rRNA, helix 69 contains pseudouridine residues at positions 1911, 1915, and 1917. The presence of these pseudouridines was found to be essential for the pH-induced conformational changes. Some of the pH-dependent changes appear to be localized to the loop region of helix 69, emphasizing the importance of the highly conserved nature of residues in this region