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TRIM25 is a multi-domain, RING-type E3 ubiquitin ligase of the tripartite motif family that has important roles in multiple RNA-dependent processes. In particular, TRIM25 functions as an effector of RIG-I and ZAP, which are innate immune sensors that recognize viral RNA and induce ubiquitin-dependent anti-viral response mechanisms. TRIM25 is reported to also bind RNA, but the molecular details of this interaction or its relevance to anti-viral defense have not been elucidated. Here, we characterize the RNA-binding activity of TRIM25 and find that the protein binds both single-stranded and double-stranded RNA. Multiple regions of TRIM25 contribute to this functionality, including the C-terminal SPRY domain and a lysine-rich motif in the linker segment connecting the SPRY and coiled-coil domains. RNA binding modulates TRIM25's ubiquitination activity in vitro, its localization in cells, and its anti-viral activity. Taken together with other studies, our results indicate that RNA binding by TRIM25 has at least three important functional consequences: by enhancing ubiquitination activity, either through allosteric effects or through clustering of multiple TRIM25 molecules; by modulating the multi-domain structure of the TRIM25 dimer, and thereby structural coupling of the SPRY and RBCC elements during the ubiquitination reaction; and by facilitating subcellular localization of the E3 ligase during virus infection.

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Background: Novel molecular markers are important diagnostic tools for the assessment of cancer progression and evaluation of effectiveness of the treatment. SOX9, a key regulator of developmental processes, is overexpressed in various neoplasms, such as prostate, breast, and colorectal cancers. However, the utilization of SOX9 as a biomarker for other urological cancers has not yet been investigated. Methods: In the present study, paired patient tissue microarrays were analyzed by immunohistochemistry, and the SOX9 protein expression was quantitated as immunoreactive scores in patients with renal cell carcinoma (RCC), bladder cancer (BCa), and penile cancer (PC). Results: In comparison with normal tissues, SOX9 protein expression was significantly upregulated in RCC (p < 0.001) and BCa (p < 0.001), and significantly correlated with the advanced pathological grade (RCC: p = 0.023) and clinical stage (RCC: p = 0.022 and BCa: p = 0.046) of patients. Based on the mRNA level in the TCGA dataset, SOX9 was upregulated in RCC with gender (p = 0.027), advanced pathological grade (p = 0.003) and advanced clinical stage (p = 0.001). Kaplan-Meier survival curves revealed that RCC patients with high SOX9 levels had shorter survival (p < 0.001). Further, high SOX9 expression was an independent prognostic factor for RCC patients (hazard ratio 0.056, 95% confidence interval 0.607-1.184; p < 0.001). Conclusion: These findings suggest that SOX9 may play an important role in tumor progression of RCC and BCa and it may be used as a biomarker of this malignancy.

TRIM5α combines distinct modes of binding into successively higher-order structures to recognize HIV-1 and retroviral capsids., TRIM5α is a restriction factor that senses incoming retrovirus cores through an unprecedented mechanism of nonself recognition. TRIM5α assembles a hexagonal lattice that avidly binds the capsid shell, which surrounds and protects the virus core. The extent to which the TRIM lattice can cover the capsid and how TRIM5α directly contacts the capsid surface have not been established. Here, we apply cryo–electron tomography and subtomogram averaging to determine structures of TRIM5α bound to recombinant HIV-1 capsid assemblies. Our data support a mechanism of hierarchical assembly, in which a limited number of basal interaction modes are successively organized in increasingly higher-order structures that culminate in a TRIM5α cage surrounding a retroviral capsid. We further propose that cage formation explains the mechanism of restriction and provides the structural context that links capsid recognition to ubiquitin-dependent processes that disable the retrovirus.

Restriction factors are intrinsic cellular defense proteins that have evolved to block microbial infections. Retroviruses such as HIV-1 are restricted by TRIM5 proteins, which recognize the viral capsid shell that surrounds, organizes, and protects the viral genome. TRIM5α uses a SPRY domain to bind capsids with low intrinsic affinity ( K D of >1 mM) and therefore requires higher-order assembly into a hexagonal lattice to generate sufficient avidity for productive capsid recognition. TRIMCyp, on the other hand, binds HIV-1 capsids through a cyclophilin A domain, which has a well-defined binding site and higher affinity ( K D of ∼10 μM) for isolated capsid subunits. Therefore, it has been argued that TRIMCyp proteins have dispensed with the need for higher-order assembly to function as antiviral factors. Here, we show that, consistent with its high degree of sequence similarity with TRIM5α, the TRIMCyp B-box 2 domain shares the same ability to self-associate and facilitate assembly of a TRIMCyp hexagonal lattice that can wrap about the HIV-1 capsid. We also show that under stringent experimental conditions, TRIMCyp-mediated restriction of HIV-1 is indeed dependent on higher-order assembly. Both forms of TRIM5 therefore use the same mechanism of avidity-driven capsid pattern recognition. IMPORTANCE Rhesus macaques and owl monkeys are highly resistant to HIV-1 infection due to the activity of TRIM5 restriction factors. The rhesus macaque TRIM5α protein blocks HIV-1 through a mechanism that requires self-assembly of a hexagonal TRIM5α lattice around the invading viral core. Lattice assembly amplifies very weak interactions between the TRIM5α SPRY domain and the HIV-1 capsid. Assembly also promotes dimerization of the TRIM5α RING E3 ligase domain, resulting in synthesis of polyubiquitin chains that mediate downstream steps of restriction. In contrast to rhesus TRIM5α, the owl monkey TRIM5 homolog, TRIMCyp, binds isolated HIV-1 CA subunits much more tightly through its cyclophilin A domain and therefore was thought to act independently of higher-order assembly. Here, we show that TRIMCyp shares the assembly properties of TRIM5α and that both forms of TRIM5 use the same mechanism of hexagonal lattice formation to promote viral recognition and restriction.

Restriction factors and pattern recognition receptors are important components of intrinsic cellular defenses against viral infection. Mammalian TRIM5α proteins are restriction factors and receptors that target the capsid cores of retroviruses and activate ubiquitin-dependent antiviral responses upon capsid recognition. Here, we report crystallographic and functional studies of the TRIM5α B-box 2 domain, which mediates higher-order assembly of TRIM5 proteins. The B-box can form both dimers and trimers, and the trimers can link multiple TRIM5α proteins into a hexagonal net that matches the lattice arrangement of capsid subunits and enables avid capsid binding. Two modes of conformational flexibility allow TRIM5α to accommodate the variable curvature of retroviral capsids. B-box mediated interactions also modulate TRIM5α’s E3 ubiquitin ligase activity, by stereochemically restricting how the N-terminal RING domain can dimerize. Overall, these studies define important molecular details of cellular recognition of retroviruses, and how recognition links to downstream processes to disable the virus. DOI: http://dx.doi.org/10.7554/eLife.16309.001, eLife digest After infecting a cell, a virus reprograms the cell to produce new copies of the virus, which then spread to other cells. However, cells have evolved ways to fight back against this infection. For example, many mammalian cells contain proteins called restriction factors that prevent the virus from multiplying. The TRIM5 proteins form one common set of restriction factors that act against a class of viruses called retroviruses. HIV-1 and related retroviruses have a protein shell known as a capsid that surrounds the genetic material of the virus. The capsid contains several hundred repeating units, each of which consists of a hexagonal ring of six capsid proteins. Although this basic pattern is maintained across different retroviruses, the overall shape of the capsids can vary considerably. For instance, HIV-1 capsids are shaped like a cone, but other retroviruses can form cylinders or spheres. Soon after a retrovirus enters a mammalian cell, TRIM5 proteins bind to the capsid. This causes the capsid to be destroyed, which prevents replication of the virus. Previous research has shown that many TRIM5 proteins must link up with each other via a region of their structure called the 'B-box 2' domain in order to efficiently recognize capsids. How this assembly process occurs, and why it enables the TRIM5 proteins to recognize different capsids was not fully understood. Now, Wagner et al. (and independently Li, Chandrasekaran et al.) have investigated these questions. Wagner et al. engineered short versions of a type of TRIM5 protein called TRIM5α and used a technique called X-ray crystallography to determine the structure of its B-box domain. This revealed that the B-box present in one molecule of TRIM5α can associate with the B-boxes on two other TRIM5α molecules. By working in groups of three (or trimers), the B-box domains connect several TRIM5α proteins to form a hexagonal net. The TRIM5α net matches the arrangement of the capsid proteins in the shell of the virus, which enables TRIM5α to bind strongly to HIV-1 capsids. Wagner et al. also found that B-box trimers are flexible, which allows the TRIM5α net to adapt to the shape of the HIV-1 capsid and wrap around regions where it curves. In addition, computer modelling suggested that the B-box trimer may also enable TRIM5α to carry out the next steps in the process of disabling the virus. Further work is now needed to understand in more detail how the trimers have this effect. DOI: http://dx.doi.org/10.7554/eLife.16309.002

Fullerene and its derivatives have been extensively studied in the biomedical field. Their biological activities towards various cell types have been reported, and previous results have implicated their potential uses as photosensitizers in photodynamic therapy of tumour and photoinactivation of bacteria and viruses, antioxidative/cytoprotective reagents and carriers for drug delivery. We describe here the effects of a BMPF (bismethanophosphonate fullerene) on matrix-related gene expression in cultured human disc cells by real-time reverse transcriptase PCR. Mediation of BMPF into water by DMSO leads to formation of an aqueous suspension of nanoparticles (denoted as nano-BMPF) with a very narrow size distribution and an average size of 136.3 nm. Moreover, nano-BMPF could induce a down-regulation of gene expression of matrix proteins aggrecan, type I collagen and type II collagen and an up-regulation of gene expression of matrix metalloproteinase 3. IL-1Ra (IL-1 receptor antagonist), but not IL-1 receptor 1, is transcriptionally inhibited by nano-BMPF. These data indicated a disc degeneration-inducing activity of nano-BMPF, raising concerns of possible adverse effects, while a fullerene-based treatment of disc diseases is employed.

Restriction factors are important components of intrinsic cellular defense mechanisms against viral pathogens. TRIM5α is a restriction factor that intercepts the incoming capsid cores of retroviruses such as HIV and provides an effective species-specific barrier to retroviral infection. The TRIM5α SPRY domain directly binds the capsid with only very weak, millimolar-level affinity, and productive capsid recognition therefore requires both TRIM5α dimerization and assembly of the dimers into a multivalent hexagonal lattice to promote avid binding. Here, we explore the important unresolved question of whether the SPRY domains are flexibly linked to the TRIM lattice or more precisely positioned to maximize avidity. Biochemical and biophysical experiments indicate that the linker segment connecting the SPRY domain to the coiled-coil domain adopts an α-helical fold, and that this helical portion mediates interactions between the two domains. Targeted mutations were generated to disrupt the putative packing interface without affecting dimerization or higher-order assembly, and we identified mutant proteins that were nevertheless deficient in capsid binding in vitro and restriction activity in cells. Our studies therefore support a model wherein substantial avidity gains during assembly-mediated capsid recognition by TRIM5α come in part from tailored spacing of tethered recognition domains., Author summary TRIM5α is a cytosolic protein that provides effective protection for mammalian cells against retroviral infection. This anti-viral defense mechanism is an unprecedented example of how the cell can recognize entire capsids, which are large, megadalton-sized particles. TRIM5α achieves this by assembling into a hexagonal scaffold that coats the capsid. An important unresolved question is how the capsid-binding SPRY domain of TRIM5α is positioned to optimize its contact points on the capsid surface. Here, we use a variety of techniques to determine that the SPRY domains in the TRIM lattice are organized in pairs and likely to be stably tethered against the hexagonal scaffold. Such an arrangement maximizes the avidity of capsid binding, and allows TRIM5α to act as a “molecular ruler” that matches the spacings and orientations of the capsid subunits.

To study the long-term curative effects of suture plus proximal gastric vagotomy (PGV) and suture plus triad-therapy (omeprazole, amoxycillin and flagyl taken orally) for the treatment of duodenal ulcer with acute perforation.Three hundred and twenty-nine patients with duodenal ulcer and acute perforation were treated with 2 different methods, respectively. Method A was suture plus PGV (group A, 153 cases), and method B was suture plus triad-therapy (group B, 176 cases). Follow-up was made by means of correspondence, outpatient reexamination and cooperation with local hospitals in 5 to 8 years after operation. The contents of follow-up included symptom acquisition (such as upper abdominal pain or distention, pyrosis, belch, acid regurgitation, vomiting, diarrhea and conditions of living or working), gastroscopy and Helicobacter pylori (HP) detection. The curative effects were evaluated by the Visick scale.Three hundred and one patients were followed up (group A 142 and group B 159). According to the Visick scale, 97 (68.3%), 19 (13.4%), 13 (9.15%) and 13 (9.15%) patients in group A, and 31 (19.5%), 28 (17.6%), 24 (15.1%) and 76 (47.8%) in group B were classified as Visick I, II, III and IV respectively (Z = -9.818, P0.01). As for HP detection, there were 130 (91.5%) patients in group A and 94 (59.1%) in group B (chi(2) = 41.438, P0.01).The long-term curative effects of suture plus PGV were superior to those of suture plus triad-therapy for duodenal ulcer with acute perforation although HP positive rate was higher in group A than in group B. HP infection is one of the etiological factors of duodenal ulcer. The increased excitability of the vagus nerve remains to play an important role in duodenal ulcer.

Xinlin Yang, Ching-Ju Li, Yueping Wan, Pinar Smith, Guowei Shang, Quanjun Cui Department of Orthopaedic Surgery, University of Virginia School of Medicine, Charlottesville, VA, USA Abstract: Antioxidants were implicated as potential reagents to enhance osteogenesis, and nano-fullerenes have been demonstrated to have a great antioxidative capacity by both in vitro and in vivo experiments. In this study, we assessed the impact of a polyhydroxylated fullerene, fullerol, on the osteogenic differentiation of human adipose-derived stem cells (ADSCs). Fullerol was not toxic against human ADSCs at concentrations up to 10 µM. At a concentration of 1 µM, fullerol reduced cellular reactive oxygen species after a 5-day incubation either in the presence or in the absence of osteogenic media. Pretreatment of fullerol for 7 days increased the osteogenic potential of human ADSCs. Furthermore, when incubated together with osteogenic medium, fullerol promoted osteogenic differentiation in a dose-dependent manner. Finally, fullerol proved to promote expression of FoxO1, a major functional isoform of forkhead box O transcription factors that defend against reactive oxygen species in bone. Although further clarification of related mechanisms is required, the findings may help further development of a novel approach for bone repair, using combined treatment of nano-fullerol with ADSCs. Keywords: polyhydroxylated fullerene, bone repair, reactive oxygen species, forkhead box protein O1