Modifying the maker : oxygenases target ribosome biology

The complexity of the eukaryotic protein synthesis machinery is partly driven by extensive and diverse modifications to associated proteins and RNAs. These modifications can have important roles in regulating translation factor activity and ribosome biogenesis and function. Further investigation of ‘translational modifications’ is warranted considering the growing evidence implicating protein synthesis as a critical point of gene expression control that is commonly deregulated in disease. New evidence suggests that translation is a major new target for oxidative modifications, specifically hydroxylations and demethylations, which generally are catalyzed by a family of emerging oxygenase enzymes that act at the interface of nutrient availability and metabolism. This review summarizes what is currently known about the role or these enzymes in targeting rRNA synthesis, protein translation and associated cellular processes

Inflammation causes remodeling of mitochondrial cytochrome c oxidase mediated by the bifunctional gene C15orf48

Dysregulated mitochondrial function is a hallmark of immune-mediated inflammatory diseases. Cytochrome c oxidase (CcO), which mediates the rate-limiting step in mitochondrial respiration, is remodeled during development and in response to changes of oxygen availability, but there has been little study of CcO remodeling during inflammation. Here, we describe an elegant molecular switch mediated by the bifunctional transcript C15orf48, which orchestrates the substitution of the CcO subunit NDUFA4 by its paralog C15ORF48 in primary macrophages. Expression of C15orf48 is a conserved response to inflammatory signals and occurs in many immune-related pathologies. In rheumatoid arthritis, C15orf48 mRNA is elevated in peripheral monocytes and proinflammatory synovial tissue macrophages, and its expression positively correlates with disease severity and declines in remission. C15orf48 is also expressed by pathogenic macrophages in severe coronavirus disease 2019 (COVID-19). Study of a rare metabolic disease syndrome provides evidence that loss of the NDUFA4 subunit supports proinflammatory macrophage functions

The Jumonji-C oxygenase JMJD7 catalyzes (3S)-lysyl hydroxylation of TRAFAC GTPases

Biochemical, structural and cellular studies reveal Jumonji-C (JmjC) domain-containing 7 (JMJD7) to be a 2-oxoglutarate (2OG)-dependent oxygenase that catalyzes (3S)-lysyl hydroxylation. Crystallographic analyses reveal JMJD7 to be more closely related to the JmjC hydroxylases than to the JmjC demethylases. Biophysical and mutation studies show that JMJD7 has a unique dimerization mode, with interactions between monomers involving both N- and C-terminal regions and disulfide bond formation. A proteomic approach identifies two related members of the translation factor (TRAFAC) family of GTPases, developmentally regulated GTP-binding proteins 1 and 2 (DRG1/2), as activity-dependent JMJD7 interactors. Mass spectrometric analyses demonstrate that JMJD7 catalyzes Fe(ii)- and 2OG-dependent hydroxylation of a highly conserved lysine residue in DRG1/2; amino-acid analyses reveal that JMJD7 catalyzes (3S)-lysyl hydroxylation. The functional assignment of JMJD7 will enable future studies to define the role of DRG hydroxylation in cell growth and disease.Fil: Markolovic, Suzana. University of Oxford; Reino UnidoFil: Zhuang, Qinqin. University Of Birmingham; Reino UnidoFil: Wilkins, Sarah E.. University of Oxford; Reino UnidoFil: Eaton, Charlotte D.. University Of Birmingham; Reino UnidoFil: Abboud, Martine I.. University of Oxford; Reino UnidoFil: Katz, Maximiliano Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: McNeil, Helen E.. University Of Birmingham; Reino UnidoFil: Leśniak, Robert K.. University of Oxford; Reino UnidoFil: Hall, Charlotte. University Of Birmingham; Reino UnidoFil: Struwe, Weston B.. University of Oxford; Reino UnidoFil: Konietzny, Rebecca. University of Oxford; Reino UnidoFil: Davis, Simon. University of Oxford; Reino UnidoFil: Yang, Ming. The Francis Crick Institute; Reino Unido. University of Oxford; Reino UnidoFil: Ge, Wei. University of Oxford; Reino UnidoFil: Benesch, Justin L. P.. University of Oxford; Reino UnidoFil: Kessler, Benedikt M.. University of Oxford; Reino UnidoFil: Ratcliffe, Peter J.. University of Oxford; Reino Unido. The Francis Crick Institute; Reino UnidoFil: Cockman, Matthew E.. The Francis Crick Institute; Reino Unido. University of Oxford; Reino UnidoFil: Fischer, Roman. University of Oxford; Reino UnidoFil: Wappner, Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Chowdhury, Rasheduzzaman. University of Stanford; Estados Unidos. University of Oxford; Reino UnidoFil: Coleman, Mathew L.. University Of Birmingham; Reino UnidoFil: Schofield, Christopher J.. University of Oxford; Reino Unid

Agglomeration of Productive Services, Industrial Structure Upgrading and Green Total Factor Productivity: An Empirical Analysis Based on 68 Prefectural-Level-and-Above Cities in the Yellow River Basin of China

Improving green total factor productivity (GTFP) is the inherent requirement for practicing the philosophy of green development and achieving regional high-quality development. Based on panel data for 68 prefectural-level-and-above cities in the Yellow River Basin of China from 2006 to 2019, we measured their GTFPs and degrees of productive-services agglomeration using the non-radial directional distance function and industrial agglomeration index formulas, respectively. Furthermore, we empirically investigated the interactive relationship between agglomeration of productive services, industrial-structure upgrading, and GTFP using the dual fixed-effects model, the mediating-effect model, and the moderating-effect model. The findings were as follows. (1) Both specialized and diversified agglomeration of productive services significantly improved the GTFPs of cities in the Yellow River Basin, and the promoting effect of specialized agglomeration was stronger than that of diversified agglomeration. (2) The diversified agglomeration of productive services (hereinafter referred to as diversified agglomeration) made a significant contribution to GTFP in all sample cities of the Yellow River Basin, while the specialized agglomeration of productive services (hereinafter referred to as specialized agglomeration) only significantly improved GTFP in the upstream cities and had no significant effect on the midstream and downstream cities. (3) When examined according to city size, specialized agglomeration was found to have a positive impact on the GTFPs of small and medium-sized cities in the Yellow River Basin but a non-significant negative impact on large cities, while the effect of diversified agglomeration on GTFP was found not to be significant. (4) Industrial-structure upgrading played partially mediating and negative moderating roles in the process of specialized agglomeration affecting the GTFPs of cities in the Yellow River Basin, but it did not become a mediating channel and moderating factor that influenced diversified agglomeration in relation to GTFP

Developmentally regulated GTPases::structure, function and roles in disease

GTPases are a large superfamily of evolutionarily conserved proteins involved in a variety of fundamental cellular processes. The developmentally regulated GTP-binding protein (DRG) subfamily of GTPases consists of two highly conserved paralogs, DRG1 and DRG2, both of which have been implicated in the regulation of cell proliferation, translation and microtubules. Furthermore, DRG1 and 2 proteins both have a conserved binding partner, DRG family regulatory protein 1 and 2 (DFRP1 and DFRP2), respectively, that prevents them from being degraded. Similar to DRGs, the DFRP proteins have also been studied in the context of cell growth control and translation. Despite these proteins having been implicated in several fundamental cellular processes they remain relatively poorly characterized, however. In this review, we provide an overview of the structural biology and biochemistry of DRG GTPases and discuss current understanding of DRGs and DFRPs in normal physiology, as well as their emerging roles in diseases such as cancer. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00018-021-03961-0

Growth Kinetic Processes of AlN Molecules on the Al-Polar Surface of AlN

National Program on Key Basic Research Project (973 Program); National Nature Science Foundation [60827004, 90921002, 60776066]; Science & Technology program of Fujian and Xiamen of ChinaWe studied growth kinetic processes of AlN molecules on the Al-polar surface of AlN using ab initio and Monte Carlo simulations. Molecular processes were presented and analyzed during the nucleation, ripening, and coalescence stages. The results show that the nucleus number decreases as temperature rises due to the increasing diffusion of the molecules. By analyzing the growth time dependence of average cluster size, interface-limited Ostwald ripening is found to be the main ripening mechanism when the temperature is lower than 1773 K. As cluster-corner crossing diffusion is limited, the growth is fractal-like extension, and the coalescence is achieved through adhesion of clusters, leading to a generally continuous morphology with some vacancies and closure failures, which is in good agreement with our experimental results. Moreover, coverage/temperature kinetic phase diagrams under different deposition rates are presented (from 0.025 to 0.1 ML/s). Our finding suggests that a temperature higher than 1800 K is crucial for growth of an ideal atomic-scale Al-polar AlN surface

Defect Suppression in AlN Epilayer Using Hierarchical Growth Units

Growing AlN layers remains a significant challenge because it is subject to a large volume fraction of grain boundaries. In this study, the nature and formation of the AlN growth mechanism is examined by ab initio simulations and experimental demonstration. The calculated formation enthalpies of the constituent elements, including the Al/N atom, Al–N molecule, and Al–N₃ cluster, vary with growth conditions in N-rich and Al-rich environments. Using the calculation results as bases, we develop a three-step metalorganic vapor-phase epitaxy, which involves the periodic growth sequence of (i) trimethylaluminum (TMAl), (ii) ammonia (NH₃), and (iii) TMAl+NH₃ supply, bringing in hierarchical growth units to improve AlN layer compactness. A series of AlN samples were grown, and their morphological and luminescent evolutions were evaluated by atomic force microscopy and cathodoluminescence, respectively. The proposed technique is advantageous because the boundaries and defect-related luminescence derived are highly depressed, serving as a productive platform from which to further optimize the properties of AlGaN semiconductors

Horizontal transmission of a multidrug-resistant IncN plasmid isolated from urban wastewater

Wastewater treatment plants (WWTPs) are considered reservoirs of antibiotic resistance genes (ARGs). Given that plasmid-mediated horizontal gene transfer plays a critical role in disseminating ARGs in the environment, it is important to inspect the transfer potential of transmissible plasmids to have a better understanding of whether these mobile ARGs can be hosted by opportunistic pathogens and should be included in One Health’s considerations. In this study, we used a fluorescent-reporter-gene based exogenous isolation approach to capture extended-spectrum beta-lactamases encoding mobile determinants from sewer microbiome samples that enter an urban water system (UWS) in Denmark. After screening and sequencing, we isolated a ∼73 Kbp IncN plasmid (pDK_DARWIN) that harboured and expressed multiple ARGs. Using a dual fluorescent reporter gene system, we showed that this plasmid can transfer into resident urban water communities. We demonstrated the transfer of pDK_DARWIN to microbiome members of both the sewer (in the upstream UWS compartment) and wastewater treatment (in the downstream UWS compartment) microbiomes. Sequence similarity search across curated plasmid repositories revealed that pDK_DARWIN derives from an IncN backbone harboured by environmental and nosocomial Enterobacterial isolates. Furthermore, we searched for pDK_DARWIN sequence matches in UWS metagenomes from three countries, revealing that this plasmid can be detected in all of them, with a higher relative abundance in hospital sewers compared to residential sewers. Overall, this study demonstrates that this IncN plasmid is prevalent across Europe and an efficient vector capable of disseminating multiple ARGs in the urban water systems