GPATCH4 regulates rRNA and snRNA 2'-O-methylation in both DHX15-dependent and DHX15-independent manners.

Regulation of RNA helicase activity, often accomplished by protein cofactors, is essential to ensure target specificity within the complex cellular environment. The largest family of RNA helicase cofactors are the G-patch proteins, but the cognate RNA helicases and cellular functions of numerous human G-patch proteins remain elusive. Here, we discover that GPATCH4 is a stimulatory cofactor of DHX15 that interacts with the DEAH box helicase in the nucleolus via residues in its G-patch domain. We reveal that GPATCH4 associates with pre-ribosomal particles, and crosslinks to the transcribed ribosomal DNA locus and precursor ribosomal RNAs as well as binding to small nucleolar- and small Cajal body-associated RNAs that guide rRNA and snRNA modifications. Loss of GPATCH4 impairs 2'-O-methylation at various rRNA and snRNA sites leading to decreased protein synthesis and cell growth. We demonstrate that the regulation of 2'-O-methylation by GPATCH4 is both dependent on, and independent of, its interaction with DHX15. Intriguingly, the ATPase activity of DHX15 is necessary for efficient methylation of DHX15-dependent sites, suggesting a function of DHX15 in regulating snoRNA-guided 2'-O-methylation of rRNA that requires activation by GPATCH4. Overall, our findings extend knowledge on RNA helicase regulation by G-patch proteins and also provide important new insights into the mechanisms regulating installation of rRNA and snRNA modifications, which are essential for ribosome function and pre-mRNA splicing.

The human RNA helicase DHX37 is required for release of the U3 snoRNP from pre-ribosomal particles.

Ribosome synthesis is an essential cellular process, and perturbation of human ribosome production is linked to cancer and genetic diseases termed ribosomopathies. During their assembly, pre-ribosomal particles undergo numerous structural rearrangements, which establish the architecture present in mature complexes and serve as key checkpoints, ensuring the fidelity of ribosome biogenesis. RNA helicases are essential mediators of such remodelling events and here, we demonstrate that the DEAH-box RNA helicase DHX37 is required for maturation of the small ribosomal subunit in human cells. Our data reveal that the presence of DHX37 in early pre-ribosomal particles is monitored by a quality control pathway and that failure to recruit DHX37 leads to pre-rRNA degradation. Using an in vivo crosslinking approach, we show that DHX37 binds directly to the U3 small nucleolar RNA (snoRNA) and demonstrate that the catalytic activity of the helicase is required for dissociation of the U3 snoRNA from pre-ribosomal complexes. This is an important event during ribosome assembly as it enables formation of the central pseudoknot structure of the small ribosomal subunit. We identify UTP14A as a direct interaction partner of DHX37 and our data suggest that UTP14A can act as a cofactor that stimulates the activity of the helicase in the context of U3 snoRNA release.

The G-patch protein NF-κB-repressing factor mediates the recruitment of the exonuclease XRN2 and activation of the RNA helicase DHX15 in human ribosome biogenesis.

In eukaryotes, the synthesis of ribosomal subunits, which involves the maturation of the ribosomal (r)RNAs and assembly of ribosomal proteins, requires the co-ordinated action of a plethora of ribosome biogenesis factors. Many of these cofactors remain to be characterized in human cells. Here, we demonstrate that the human G-patch protein NF-κB-repressing factor (NKRF) forms a pre-ribosomal subcomplex with the DEAH-box RNA helicase DHX15 and the 5΄-3΄ exonuclease XRN2. Using UV crosslinking and analysis of cDNA (CRAC), we reveal that NKRF binds to the transcribed spacer regions of the pre-rRNA transcript. Consistent with this, we find that depletion of NKRF, XRN2 or DHX15 impairs an early pre-rRNA cleavage step (A'). The catalytic activity of DHX15, which we demonstrate is stimulated by NKRF functioning as a cofactor, is required for efficient A' cleavage, suggesting that a structural remodelling event may facilitate processing at this site. In addition, we show that depletion of NKRF or XRN2 also leads to the accumulation of excised pre-rRNA spacer fragments and that NKRF is essential for recruitment of the exonuclease to nucleolar pre-ribosomal complexes. Our findings therefore reveal a novel pre-ribosomal subcomplex that plays distinct roles in the processing of pre-rRNAs and the turnover of excised spacer fragments.

Protein cofactor competition regulates the action of a multifunctional RNA helicase in different pathways.

A rapidly increasing number of RNA helicases are implicated in several distinct cellular processes, however, the modes of regulation of multifunctional RNA helicases and their recruitment to different target complexes have remained unknown. Here, we show that the distribution of the multifunctional DEAH-box RNA helicase Prp43 between its diverse cellular functions can be regulated by the interplay of its G-patch protein cofactors. We identify the orphan G-patch protein Cmg1 (YLR271W) as a novel cofactor of Prp43 and show that it stimulates the RNA binding and ATPase activity of the helicase. Interestingly, Cmg1 localizes to the cytoplasm and to the intermembrane space of mitochondria and its overexpression promotes apoptosis. Furthermore, our data reveal that different G-patch protein cofactors compete for interaction with Prp43. Changes in the expression levels of Prp43-interacting G-patch proteins modulate the cellular localization of Prp43 and G-patch protein overexpression causes accumulation of the helicase in the cytoplasm or nucleoplasm. Overexpression of several G-patch proteins also leads to defects in ribosome biogenesis that are consistent with withdrawal of the helicase from this pathway. Together, these findings suggest that the availability of cofactors and the sequestering of the helicase are means to regulate the activity of multifunctional RNA helicases and their distribution between different cellular processes.

Effects of titanium-based nanotube films on osteoblast behavior in vitro.

One of the major research interests of nanomedicine is the designing of harmless and biocompatible medical devices. To improve the features of Ti surface, TiO2 based nanotube (TNT) films (50 nm diameter) achieved by anodic oxidation and thermal treatment were grown on titanium and on Ti6Al4V and Ti6Al7Nb alloys. Their in vitro toxicity and biocompatibility were investigated using G292 osteoblast cell line. The LDH release after 24 and 48 h of exposure demonstrated that TNT layers were not cytotoxic. The cell growth on TNT films deposited on titanium and Ti6Al4V was significantly increased compared with Ti6Al7Nb. F-actin staining showed a better organized actin cytoskeleton in osteoblasts grown on these two samples, which provide the best conditions for osteoblast attachment and spreading. Analysis of GSH distribution revealed a higher nuclear level in the samples with TNTs compared with Ti plate without nanotubes, indicating an active proliferation. Thus, nuclear glutathione levels can be used as a useful biomarker for biocompatibility assessment. Our results suggest that the substrate for TNTs can have a significant impact on cell morphology and fate. In conclusion, the TNT/Ti and TNT/Ti6Al4V were toxicity-free and can provide a proper nanostructure for a positive cell response.

Si/SiO2 quantum dots cause cytotoxicity in lung cells through redox homeostasis imbalance.

Si/SiO2 quantum dots (QDs) are novel particles with unique physicochemical properties that promote them as potential candidates for biomedical applications. Although their interaction with human cells has been poorly investigated, oxidative stress appears to be the main factor involved in the cytotoxicity of these nanoparticles. In this study, we show for the first time the influence of Si/SiO2 QDs on cellular redox homeostasis and glutathione distribution in human lung fibroblasts. The nanoparticles morphology, composition and structure have been investigated using high resolution transmission electron microscopy (HRTEM), selected area electron diffraction (SAED), energy-dispersive X-ray spectroscopy (EDX) and X-ray diffraction (XRD) analysis. MRC-5 cells (human lung fibroblasts) were incubated with various concentrations of Si/SiO2 QDs ranging between 25 and 200 µg/mL for up to 72 h. The results of the MTT and sulforhodamine B assays showed that exposure to QDs led to a time-dependent decrease in cell viability and biomass. The increase in reactive oxygen species (ROS) and malondialdehyde (MDA) levels together with the lower glutathione content suggested that the cellular redox homeostasis was altered. Regarding GSH distribution, the first two days of treatment resulted in a localization of GSH mainly in the cytoplasm, while at longer incubation time the nuclear/cytoplasmic ratio indicated a nuclear localization. These modifications of cell redox state also affected the redox status of proteins, which was demonstrated by the accumulation of oxidized proteins and actin S-glutathionylation. In addition, the externalization of phosphatidylserine provided evidence that apoptosis might be responsible for cell death, but necrosis was also revealed. Our results suggest that Si/SiO2 quantum dots exerted cytotoxicity on MRC-5 cells by disturbing cellular homeostasis which had an effect upon protein redox status.