Human RioK3 is a novel component of cytoplasmic pre-40S pre-ribosomal particles

Maturation of the 40S ribosomal subunit precursors in mammals mobilizes several non-ribosomal proteins, including the atypical protein kinase RioK2. Here, we have investigated the involvement of another member of the RIO kinase family, RioK3, in human ribosome biogenesis. RioK3 is a cytoplasmic protein that does not seem to shuttle between nucleus and cytoplasm via a Crm1-dependent mechanism as does RioK2 and which sediments with cytoplasmic 40S ribosomal particles in a sucrose gradient. When the small ribosomal subunit biogenesis is impaired by depletion of either rpS15, rpS19 or RioK2, a concomitant decrease in the amount of RioK3 is observed. Surprisingly, we observed a dramatic and specific increase in the levels of RioK3 when the biogenesis of the large ribosomal subunit is impaired. A fraction of RioK3 is associated with the non ribosomal pre-40S particle components hLtv1 and hEnp1 as well as with the 18S-E pre-rRNA indicating that it belongs to a bona fide cytoplasmic pre-40S particle. Finally, RioK3 depletion leads to an increase in the levels of the 21S rRNA precursor in the 18S rRNA production pathway. Altogether, our results strongly suggest that RioK3 is a novel cytoplasmic component of pre-40S pre-ribosomal particle(s) in human cells, required for normal processing of the 21S pre-rRNA

Hypoxic regulation of RIOK3 is a major mechanism for cancer cell invasion and metastasis.

Hypoxia is a common feature of locally advanced breast cancers that is associated with increased metastasis and poorer survival. Stabilisation of hypoxia-inducible factor-1α (HIF1α) in tumours causes transcriptional changes in numerous genes that function at distinct stages of the metastatic cascade. We demonstrate that expression of RIOK3 (RIght Open reading frame kinase 3) was increased during hypoxic exposure in an HIF1α-dependent manner. RIOK3 was localised to distinct cytoplasmic aggregates in normoxic cells and underwent redistribution to the leading edge of the cell in hypoxia with a corresponding change in the organisation of the actin cytoskeleton. Depletion of RIOK3 expression caused MDA-MB-231 to become elongated and this morphological change was due to a loss of protraction at the trailing edge of the cell. This phenotypic change resulted in reduced cell migration in two-dimensional cultures and inhibition of cell invasion through three-dimensional extracellular matrix. Proteomic analysis identified interactions of RIOK3 with actin and several actin-binding factors including tropomyosins (TPM3 and TPM4) and tropomodulin 3. Depletion of RIOK3 in cells resulted in fewer and less organised actin filaments. Analysis of these filaments showed reduced association of TPM3, particularly during hypoxia, suggesting that RIOK3 regulates actin filament specialisation. RIOK3 depletion reduced the dissemination of MDA-MB-231 cells in both a zebrafish model of systemic metastasis and a mouse model of pulmonary metastasis. These findings demonstrate that RIOK3 is necessary for maintaining actin cytoskeletal organisation required for migration and invasion, biological processes that are necessary for hypoxia-driven metastasis

Bacterial Bioluminescence: Light Emission in Photobacterium phosphoreum Is Not Under Quorum-Sensing Control

International audienceBacterial-bioluminescence regulation is often associated with quorum sensing. Indeed, many studies have been made on this subject and indicate that the expression of the light-emission-involved genes is density dependent. However, most of these studies have concerned two model species, Aliivibrio fischeri and Vibrio campbellii. Very few works have been done on bioluminescence regulation for the other bacterial genera. Yet, according to the large variety of habitats of luminous marine bacteria, it would not be surprising to find different light-regulation systems. In this study, we used Photobacterium phosphoreum ANT-2200, a piezophilic bioluminescent strain isolated from Mediterranean deep-sea waters (2200-m depth). To answer the question of whether or not the bioluminescence of P. phosphoreum ANT-2200 is under quorum-sensing control, we focused on the correlation between growth and light emission through physiological, genomic and, transcriptomic approaches. Unlike A. fischeri and V. campbellii, the light of P. phosphoreum ANT-2200 immediately increases from its initial level. Interestingly, the emitted light increases at much higher rate at the low cell density than it does for higher cell-density values. The expression level of the light-emission-involved genes stays constant all along the exponential growth phase. We also showed that, even when more light is produced, when the strain is cultivated at high hydrostatic pressure, no change in the transcription level of these genes can be detected. Through different experiments and approaches, our results clearly indicate that, under the tested conditions, the genes, directly involved in the bioluminescence in P. phosphoreum ANT-2200, are not controlled at a transcriptomic level. Quite obviously, these results demonstrate that the light emission of the strain is not density dependent, which means not under quorum-sensing control. Through this study, we point out that bacterial-bioluminescence regulation should not, from now on, be always linked with the quorum-sensing control

Patients and Parents’ Experience of Multi-Family Therapy for Anorexia Nervosa: A Pilot Study

International audienceBackground: Family therapy is considered as the gold standard in treatment of adolescents with anorexia nervosa (AN). Among the different types of family therapy, multi-family therapy (MFT) is increasingly used for treating AN, and shows promising results. In this article, our focus relied on the patients’ and their parents’ perceptions of the effectiveness and the underlying mechanisms of the MFT. Methods: The present pilot exploratory qualitative study included two focus groups conducted using a semi-structured approach: one with the adolescents ( n = 3), and another with one or two of their parents ( n = 4 mothers; n = 2 fathers). The subjects discussed were the changes observed in both AN symptoms and family interactions following therapy, and the mechanisms underlying these changes. We crossed the perspectives of the adolescents and of the parents on these two points. Results: Qualitative analysis revealed that while both adolescents and parents had difficulties relating the changes they observed in the last year to MFT, they were able to say that the group cohesion had several positive effects and that their family dynamics had improved. In the light of analysis the adolescents perceived more improvements related eating disorders symptoms than their parents did, while parents were concerned about a negative effect of MFT on their children. Discussion: While both patients and parents perceived improvements in both AN symptoms and family interactions in the past year, it was not clear if they considered MFT to have led to these improvements. FG also explored the MFT mechanisms underlying changes. Both adolescents and their parents stressed the beneficial effects of identification to others members of the group and shared experience to overcome social isolation. Parents also mentioned the sympathy they felt for each other. The idea that they give a central place to families in the therapy was also described by the families

A RUpture‐Based detection method for the Active mesopeLagIc Zone (RUBALIZ): A crucial step toward rigorous carbon budget assessments

Determining mesopelagic organic carbon budgets is essential to characterize the ocean's role as a carbon dioxide sink. This is because the biological processes observed in the mesopelagic zone are crucial for understanding the biological carbon pump. Yet, field assessments of carbon budgets are often unbalanced with the carbon demand exceeding its supply. This underlines either methodological issues in the budget calculations or incomplete knowledge of the mesopelagic carbon cycling with potentially missing sources. Carbon budgets are built by partitioning the ocean into vertical depth zones. Vertical boundaries are conventionally defined between 200 and 1000 m depth or using various thresholds. Such approaches lack consistent methodology preventing robust comparison of mesopelagic carbon budget from region to region. Here, using a statistical rupture detection method applied to conductivity–temperature–depth (CTD)-cast variables (fluorescence, O2 concentration, potential temperature, salinity, and density), we aim to provide independent estimates of mesopelagic boundaries. We demonstrate that the so-determined upper boundary is highly correlated with the knee points of the particulate organic carbon (POC) fluxes estimated by a power law and that over 90% of the POC flux attenuation occurs within our method boundaries. The identified zone therefore corresponds to the most active part of the conventional mesopelagic zone and we name it the “active mesopelagic zone” (AMZ). We find that the depths of the mesopelagic zone depend on the region considered. Our results demonstrate that the mesopelagic carbon budget discrepancy can vary up to four folds depending on the boundaries chosen and hence provide novel grounds to reassess existing and future mesopelagic carbon budgets

The Rio1p ATPase hinders premature entry into translation of late pre-40S pre-ribosomal particles

International audienc

The Rio1p ATPase hinders premature entry into translation of late pre-40S pre-ribosomal particles

Cytoplasmic maturation of precursors to the small ribosomal subunit in yeast requires the intervention of a dozen assembly factors (AFs), the precise roles of which remain elusive. One of these is Rio1p that seems to intervene at a late step of pre-40S particle maturation. We have investigated the role played by Rio1p in the dynamic association and dissociation of AFs with and from pre-40S particles. Our results indicate that Rio1p depletion leads to the stalling of at least 4 AFs (Nob1p, Tsr1p, Pno1p/Dim2p and Fap7p) in 80S-like particles. We conclude that Rio1p is important for the timely release of these factors from 80S-like particles. In addition, we present immunoprecipitation and electron microscopy evidence suggesting that when Rio1p is depleted, a subset of Nob1p-containing pre-40S particles associate with translating polysomes. Using Nob1p as bait, we purified pre-40S particles from cells lacking Rio1p and performed ribosome profiling experiments which suggest that immature 40S subunits can carry out translation elongation. We conclude that lack of Rio1p allows premature entry of pre-40S particles in the translation process and that the presence of Nob1p and of the 18S rRNA 3 extension in the 20S pre-rRNA is not incompatible with translation elongation

Mesopelagic microbial carbon production correlates with diversity across different marine particle fractions

International audienceThe vertical flux of marine snow particles significantly reduces atmospheric carbon dioxide concentration. In the mesopelagic zone, a large proportion of the organic carbon carried by sinking particles dissipates thereby escaping long term sequestration. Particle associated prokaryotes are largely responsible for such organic carbon loss. However, links between this important ecosystem flux and ecological processes such as community development of prokaryotes on different particle fractions (sinking vs. non-sinking) are yet virtually unknown. This prevents accurate predictions of mesopelagic organic carbon loss in response to changing ocean dynamics. Using combined measurements of prokaryotic heterotrophic production rates and species richness in the North Atlantic, we reveal that carbon loss rates and associated microbial richness are drastically different with particle fractions. Our results demonstrate a strong negative correlation between prokaryotic carbon losses and species richness. Such a trend may be related to prokaryotes detaching from fast-sinking particles constantly enriching non-sinking associated communities in the mesopelagic zone. Existing global scale data suggest this negative correlation is a widespread feature of mesopelagic microbes

A novel method to sample individual marine snow particles for downstream molecular analyses

Abstract The ocean–atmosphere exchange of carbon largely depends on the balance between carbon export of particulate organic carbon (POC) as sinking marine particles, and POC remineralization by attached microbial communities. Despite the vast spectrum of types, sources, ages, shapes, and composition of individual sinking particles, they are usually considered as a bulk together with their associated microbial communities. This limits our mechanistic understanding of the biological carbon pump (BCP) and its feedback on the global carbon cycle. We established a method to sample individual particles while preserving their shape, structure, and nucleic acids by placing a jellified RNA‐fixative at the bottom of drifting sediment traps. Coupling imaging of individual particles with associated 16S rRNA analysis reveals that active bacterial communities are highly heterogenous from one particles origin to another. In contrast to lab‐made particles, we found that complex in situ conditions lead to heterogeneity even within the same particle type. Our new method allows to associate patterns of active prokaryotic and functional diversity to particle features, enabling the detection of potential remineralization niches. This new approach will therefore improve our understanding of the BCP and numerical representation in the context of a rapidly changing ocean