Targeting the conserved active site of splicing machines with specific and selective small molecule modulators.

The self-splicing group II introns are bacterial and organellar ancestors of the nuclear spliceosome and retro-transposable elements of pharmacological and biotechnological importance. Integrating enzymatic, crystallographic, and simulation studies, we demonstrate how these introns recognize small molecules through their conserved active site. These RNA-binding small molecules selectively inhibit the two steps of splicing by adopting distinctive poses at different stages of catalysis, and by preventing crucial active site conformational changes that are essential for splicing progression. Our data exemplify the enormous power of RNA binders to mechanistically probe vital cellular pathways. Most importantly, by proving that the evolutionarily-conserved RNA core of splicing machines can recognize small molecules specifically, our work provides a solid basis for the rational design of splicing modulators not only against bacterial and organellar introns, but also against the human spliceosome, which is a validated drug target for the treatment of congenital diseases and cancers.

Quantifying the cost savings and health impacts of improving colonoscopy quality: an economic evaluation.

OBJECTIVE: To estimate and quantify the cost implications and health impacts of improving the performance of English endoscopy services to the optimum quality as defined by postcolonoscopy colorectal cancer (PCCRC) rates. DESIGN: A semi-Markov state-transition model was constructed, following the logical treatment pathway of individuals who could potentially undergo a diagnostic colonoscopy. The model consisted of three identical arms, each representing a high, middle or low-performing trust's endoscopy service, defined by PCCRC rates. A cohort of 40-year-old individuals was simulated in each arm of the model. The model's time horizon was when the cohort reached 90 years of age and the total costs and quality-adjusted life-years (QALYs) were calculated for all trusts. Scenario and sensitivity analyses were also conducted. RESULTS: A 40-year-old individual gains 0.0006 QALYs and savings of £6.75 over the model lifetime by attending a high-performing trust compared with attending a middle-performing trust and gains 0.0012 QALYs and savings of £14.64 compared with attending a low-performing trust. For the population of England aged between 40 and 86, if all low and middle-performing trusts were improved to the level of a high-performing trust, QALY gains of 14 044 and cost savings of £249 311 295 are possible. Higher quality trusts dominated lower quality trusts; any improvement in the PCCRC rate was cost-effective. CONCLUSION: Improving the quality of endoscopy services would lead to QALY gains among the population, in addition to cost savings to the healthcare provider. If all middle and low-performing trusts were improved to the level of a high-performing trust, our results estimate that the English National Health Service would save approximately £5 million per year.

Does destination make a difference? Outcomes after a policy change affecting cutoff times for pre-hospital transport.

BACKGROUND: Facilitating primary triage and care at Pediatric Trauma Centers (PTCs) can improve outcomes for children after trauma. However, scene location and regional EMS regulations may result in initial evaluation occurring at non-pediatric facilities with later transportation to PTCs for definitive care. In this study, we assessed the results of a change in transport time cutoff from 30 to 45 minutes on pediatric patient outcomes. METHODS: After IRB approval, the Pediatric Trauma Database at a level 1 PTC was queried for patients seen before (January 1, 2015-December 31, 2017) and after (January 1, 2018-December 31, 2020) the implementation of a policy increasing transport cutoff time from 30 to 45 minutes. Patient outcomes were compared by transport status and ISS using generalized linear regression analysis. RESULTS: 505 patients were seen pre and 413 patients post policy changes. Both groups had similar numbers of severely injured patients (ISS ≥ 15, 64 (13%) pre and 61 (15%) post). Average transport time increased post change (pre 20 min (95% CI[18,22] min), post 29 min (95% CI[26,33] min, p = 0.0252), consistent with policy compliance. The proportion of transferred patients did not change after policy implementation (p = 0.5856), and the complications among all patients with ISS ≥ 15 did not significantly decrease (pre 75%, post 65.6%). However, those patients with ISS ≥ 15 admitted directly from the scene had a lower frequency of complications after the policy changes (pre 76%, post 59%, p = 0.0319), and in the post period transferred patients with an ISS ≥ 15 had a higher complication rate than those admitted directly from the scene (p < 0.0001). CONCLUSIONS: Direct scene admission to a PTC is associated with a lower complication profile for patients with higher ISS. Methods to ensure adherence to cutoff thresholds for EMS transport may have a positive benefit on patient outcomes. LEVEL OF EVIDENCE: IV, prognostic/epidemiological.

Costs of endovascular and open repair of thoracic aortic aneurysms.

BACKGROUND: Repair of thoracic aortic aneurysms with either endovascular repair (TEVAR) or open surgical repair (OSR) represents major surgery, is costly and associated with significant complications. The aim of this study was to establish accurate costs of delivering TEVAR and OSR in a cohort of UK NHS patients suitable for open and endovascular treatment for the whole treatment pathway from admission and to discharge and 12-month follow-up. METHODS: A prospective study of UK NHS patients from 30 NHS vascular/cardiothoracic units in England aged ≥18, with distal arch/descending thoracic aortic aneurysms (CTAA) was undertaken. A multicentre prospective cost analysis of patients (recruited March 2014-July 2018, follow-up until July 2019) undergoing TEVAR or OSR was performed. Patients deemed suitable for open or endovascular repair were included in this study. A micro-costing approach was adopted. RESULTS: Some 115 patients having undergone TEVAR and 35 patients with OSR were identified. The mean (s.d.) cost of a TEVAR procedure was higher £26 536 (£9877) versus OSR £17 239 (£8043). Postoperative costs until discharge were lower for TEVAR £7484 (£7848) versus OSR £28 636 (£23 083). Therefore, total NHS costs from admission to discharge were lower for TEVAR £34 020 (£14 301), versus OSR £45 875 (£43 023). However, mean NHS costs for 12 months following the procedure were slightly higher for the TEVAR £5206 (£11 585) versus OSR £5039 (£11 994). CONCLUSIONS: Surgical procedure costs were higher for TEVAR due to device costs. Total in-hospital costs were higher for OSR due to longer hospital and critical care stay. Follow-up costs over 12 months were slightly higher for TEVAR due to hospital readmissions.

Robotic and laparoscopic gynaecological surgery: a prospective multicentre observational cohort study and economic evaluation in England.

OBJECTIVE: To compare the health-related quality of life and cost-effectiveness of robot-assisted laparoscopic surgery (RALS) versus conventional 'straight stick' laparoscopic surgery (CLS) in women undergoing hysterectomy as part of their treatment for either suspected or proven gynaecological malignancy. DESIGN: Multicentre prospective observational cohort study. SETTING: Patients aged 16+ undergoing hysterectomy as part of their treatment for gynaecological malignancy at 12 National Health Service (NHS) cancer units and centres in England between August 2017 and February 2020. PARTICIPANTS: 275 patients recruited with 159 RALS, 73 CLS eligible for analysis. OUTCOME MEASURES: Primary outcome was the European Organisation for Research and Treatment of Cancer Quality of Life measure (EORTC). Secondary outcomes included EuroQol-5 Dimension (EQ-5D-5L) utility, 6-minute walk test (6MWT), NHS costs using pounds sterling (£) 2018-2019 prices and cost-effectiveness. The cost-effectiveness evaluation compared EQ-5D-5L quality adjusted life years and costs between RALS and CLS. RESULTS: No difference identified between RALS and CLS for EORTC, EQ-5D-5L utility and 6MWT. RALS had unadjusted mean cost difference of £556 (95% CI -£314 to £1315) versus CLS and mean quality adjusted life year (QALY) difference of 0.0024 (95% CI -0.00051 to 0.0057), non-parametric incremental cost-effectiveness ratio of £231 667per QALY. For the adjusted cost-effectiveness analysis, RALS dominated CLS with a mean cost difference of -£188 (95% CI -£1321 to £827) and QALY difference of 0.0024 (95% CI -0.0008 to 0.0057). CONCLUSIONS: Findings suggest that RALS versus CLS in women undergoing hysterectomy (after adjusting for differences in morbidity) is cost-effective with lower costs and QALYs. Results are highly sensitive to the usage of robotic hardware with higher usage increasing the probability of cost-effectiveness. Non-inferiority randomised controlled trial would be of benefit to decision-makers to provide further evidence on the cost-effectiveness of RALS versus CLS but may not be practical due to surgical preferences of surgeons and the extensive roll out of RALS.

BioSAXS at European Synchrotron Radiation Facility - Extremely Brilliant Source: BM29 with an upgraded source, detector, robot, sample environment, data collection and analysis software.

As part of its Extremely Brilliant Source (EBS) upgrade project, the ESRF's BM29 BioSAXS beamline was subject to a significant upgrade and refurbishment. In addition to the replacement of the beamline's original bending magnet source by a two-pole wiggler, leading to an increase in brilliance by a factor of 60, the sample environment of the beamline was almost completely refurbished: a vacuum-compatible Pilatus3 X 2M with a sensitive area of 253.7 mm × 288 mm and frame rates up to 250 Hz was installed, increasing the active area available and thus the q-scaling of scattering images taken; the sample changer was replaced with an upgraded version, allowing more space for customizable sample environments and the installation of two new sample exposure units; the software associated with the beamline was also renewed. In addition, the layout and functionality of the BSXCuBE3 (BioSAXS Customized Beamline Environment) data acquisition software was redesigned, providing an intuitive `user first' approach for inexperienced users, while at the same time maintaining more powerful options for experienced users and beamline staff. Additional features of BSXCuBE3 are queuing of samples; either consecutive sample changer and/or SEC-SAXS (size-exclusion chromatography small-angle X-ray scattering) experiments, including column equilibration were also implemented. Automatic data processing and analysis are now managed via Dahu, an online server with upstream data reduction, data scaling and azimuthal integration built around PyFAI (Python Fast Azimuthal Integration), and data analysis performed using the open source FreeSAS. The results of this automated data analysis pipeline are displayed in ISPyB/ExiSAXS. The upgraded BM29 has been in operation since the post-EBS restart in September 2020, and here a full description of its new hardware and software characteristics together with examples of data obtained are provided.

The impact of a digital joint school educational programme on post-operative outcomes following lower limb arthroplasty: a retrospective comparative cohort study.

BACKGROUND: As part of an ongoing service improvement project, a digital 'joint school' (DJS) was developed to provide education and support to patients undergoing total hip (THR) and total knee (TKR) replacement surgery. The DJS allowed patients to access personalised care plans and educational resources using web-enabled devices, from being listed for surgery until 12 months post-operation. The aim of this study was to compare a cohort of patients enrolled into the DJS with a cohort of patients from the same NHS trust who received a standard 'non-digital' package of education and support in terms of Health-Related Quality of Life (HRQoL), functional outcomes and hospital length of stay (LoS). METHODS: A retrospective comparative cohort study of all patients undergoing primary TKR/THR at a single NHS trust between 1st Jan 2018 and 31st Dec 2019 (n = 2406) was undertaken. The DJS was offered to all patients attending the clinics of early adopting surgeons and the remaining surgeons offered their patient's standard written and verbal information. This allowed comparison between patients that received the DJS (n = 595) and those that received standard care (n = 1811). For each patient, demographic data, LoS and patient reported outcome measures (EQ-5D-3L, Oxford hip/knee scores (OKS/OHS)) were obtained. Polynomial regressions, adjusting for age, sex, Charlson Comorbidity Index (CCI) and pre-operative OKS/OHS or EQ-5D, were used to compare the outcomes for patients receiving DJS and those receiving standard care. FINDINGS: Patients that used the DJS had greater improvements in their EQ-5D, and OKS/OHS compared to patients receiving standard care for both TKR and THR (EQ-5D difference: TKR coefficient estimate (est) = 0.070 (95%CI 0.004 to 0.135); THR est = 0.114 (95%CI 0.061 to 0.166)) and OKS/OHS difference: TKR est = 5.016 (95%CI 2.211 to 7.820); THR est = 4.106 (95%CI 2.257 to 5.955)). The DJS had a statistically significant reduction on LoS for patients who underwent THR but not TKR. CONCLUSION: The use of a DJS was associated with improved functional outcomes when compared to a standard 'non-digital' method. The improvements between pre-operative and post-operative outcomes in EQ-5D and OKS/OHS were higher for patients using the DJS. Furthermore, THR patients also had a shorter LoS.

Biallelic pathogenic variants in roundabout guidance receptor 1 associate with syndromic congenital anomalies of the kidney and urinary tract.

Congenital anomalies of the kidney and urinary tract (CAKUT) represent the most common cause of chronic kidney failure in children. Despite growing knowledge of the genetic causes of CAKUT, the majority of cases remain etiologically unsolved. Genetic alterations in roundabout guidance receptor 1 (ROBO1) have been associated with neuronal and cardiac developmental defects in living individuals. Although Slit-Robo signaling is pivotal for kidney development, diagnostic ROBO1 variants have not been reported in viable CAKUT to date. By next-generation-sequencing methods, we identified six unrelated individuals and two non-viable fetuses with biallelic truncating or combined missense and truncating variants in ROBO1. Kidney and genitourinary manifestation included unilateral or bilateral kidney agenesis, vesicoureteral junction obstruction, vesicoureteral reflux, posterior urethral valve, genital malformation, and increased kidney echogenicity. Further clinical characteristics were remarkably heterogeneous, including neurodevelopmental defects, intellectual impairment, cerebral malformations, eye anomalies, and cardiac defects. By in silico analysis, we determined the functional significance of identified missense variants and observed absence of kidney ROBO1 expression in both human and murine mutant tissues. While its expression in multiple tissues may explain heterogeneous organ involvement, variability of the kidney disease suggests gene dosage effects due to a combination of null alleles with mild hypomorphic alleles. Thus, comprehensive genetic analysis in CAKUT should include ROBO1 as a new cause of recessively inherited disease. Hence, in patients with already established ROBO1-associated cardiac or neuronal disorders, screening for kidney involvement is indicated.

Aneurysm growth, survival, and quality of life in untreated thoracic aortic aneurysms: the effective treatments for thoracic aortic aneurysms study.

AIMS: To observe, describe, and evaluate management and timing of intervention for patients with untreated thoracic aortic aneurysms. METHODS AND RESULTS: Prospective study of UK National Health Service (NHS) patients aged ≥18 years, with new/existing arch or descending thoracic aortic aneurysms of ≥4 cm diameter, followed up until death, intervention, withdrawal, or July 2019. Outcomes were aneurysm growth, survival, quality of life (using the EQ-5D-5L utility index), and hospital admissions. Between 2014 and 2018, 886 patients were recruited from 30 NHS vascular/cardiothoracic units. Maximum aneurysm diameter was in the descending aorta in 725 (82%) patients, growing at 0.2 cm (0.17-0.24) per year. Aneurysms of ≥4 cm in the arch increased by 0.07 cm (0.02-0.12) per year. Baseline diameter was related to age and comorbidities, and no clinical correlates of growth were found. During follow-up, 129 patients died, 64 from aneurysm-related events. Adjusting for age, sex, and New York Heart Association dyspnoea index, risk of death increased with aneurysm size at baseline [hazard ratio (HR): 1.88 (95% confidence interval: 1.64-2.16) per cm, P < 0.001] and with growth [HR: 2.02 (1.70-2.41) per cm, P < 0.001]. Hospital admissions increased with aneurysm size [relative risk: 1.21 (1.05-1.38) per cm, P = 0.008]. Quality of life decreased annually for each 10-year increase in age [-0.013 (-0.019 to -0.007), P < 0.001] and for current smoking [-0.043 (-0.064 to -0.023), P = 0.004]. Aneurysm size was not associated with change in quality of life. CONCLUSION: International guidelines should consider increasing monitoring intervals to 12 months for small aneurysms and increasing intervention thresholds. Individualized decisions about surveillance/intervention should consider age, sex, size, growth, patient characteristics, and surgical risk.

Systematic review of endovascular stent grafting versus open surgical repair for the elective treatment of arch/descending thoracic aortic aneurysms.

OBJECTIVE: To review comparisons of the effectiveness of endovascular stent grafting (ESG) against open surgical repair (OSR) for treatment of chronic arch or descending thoracic aortic aneurysms (TAA). DESIGN: Systematic review and meta-analysis DATA SOURCES: MEDLINE, EMBASE, CENTRAL, WHO International Clinical Trials Routine data collection, current controlled trials, clinical trials and the NIHR portfolio were searched from January 1994 to March 2020. ELIGIBILITY CRITERIA FOR SELECTIVE STUDIES: All identified studies that compared ESG and OSR, including randomised controlled trials (RCTs), quasi-randomised and non-RCTs, comparative cohort studies and case-control studies matched on main outcomes were sought. Participants had to receive elective treatments for arch/descending (TAA). Studies were excluded where other thoracic aortic conditions (eg, rupture or dissection) were reported, unless results for patients receiving elective treatment for arch/descending TAA reported separately. DATA EXTRACTION AND SYNTHESIS: Data were extracted by one reviewer and checked by another. Risk of Bias was assessed using the ROBINS-I tool. Meta-analysis was conducted using random effects. Where meta-analysis not appropriate, results were reported narratively. RESULTS: Five comparative cohort studies met inclusion criteria, reporting 3955 ESG and 21 197 OSR patients. Meta-analysis of unadjusted short-term (30 day) all-cause mortality favoured ESG (OR 0.75; 95% CI 0.55 to 1.03)). Heterogeneity identified between larger and smaller studies. Sensitivity analysis of four studies including only descending TAA showed no statistical significance (OR 0.73, 95% CI 0.45 to 1.18)), moderate heterogeneity. Meta-analysis of adjusted short-term all-cause mortality favoured ESG (OR 0.71, 95% CI 0.51 to 0.98)), no heterogeneity. Longer-term (beyond 30 days) survival from all-cause mortality favoured OSR in larger studies and ESG in smaller studies. Freedom from reintervention in the longer-term favoured OSR. Studies reporting short-term non-fatal complications suggest fewer events following ESG. CONCLUSIONS: There is limited and increasingly dated evidence on the comparison of ESG and OSR for treatment of arch/descending TAA. PROSPERO REGISTRATION NUMBER: CRD42017054565.

Decapping Enzyme NUDT12 Partners with BLMH for Cytoplasmic Surveillance of NAD-Capped RNAs.

RNA polymerase II transcripts receive a protective 5',5'-triphosphate-linked 7-methylguanosine (m7G) cap, and its removal by decapping enzymes like DCP2 is critical for initiation of RNA decay. Alternative RNA caps can be acquired when transcription initiation uses metabolites like nicotinamide adenine dinucleotide (NAD), generating NAD-RNAs. Here, we identify human NUDT12 as a cytosolic NAD-RNA decapping enzyme. NUDT12 is active only as homodimers, with each monomer contributing to creation of the two functional catalytic pockets. We identify an ∼600-kDa dodecamer complex between bleomycin hydrolase (BLMH) and NUDT12, with BLMH being required for localization of NUDT12 to a few discrete cytoplasmic granules that are distinct from P-bodies. Both proteins downregulate gene expression when artificially tethered to a reporter RNA in vivo. Furthermore, loss of Nudt12 results in a significant upregulation of circadian clock transcripts in mouse liver. Overall, our study points to a physiological role for NUDT12 in the cytosolic surveillance of NAD-RNAs.

Non-Communicable Disease Risk Factors Among a Cohort of Mine Workers in Mongolia.

OBJECTIVE: Prevalence of non-communicable diseases (NCD) is growing among workers globally, causing 71% of all premature deaths. We determined baseline prevalence of risk factors among mine workers. METHOD: One thousand one hundred sixty-nine employees were randomly recruited to a cross-sectional study. The study focused on key risk factors of hypertension, obesity, alcohol use, and smoking status. These factors are known key contributors to NCD risk. RESULTS: Results of the study showed prevalence's of hypertension 12.9%, obesity 64.1%, alcohol users 22.1%, and smokers 38.8%. The general population prevalence's are 27.5%, 56.8%, 15.5%, and 24.8%, respectively. CONCLUSION: Prevalence of hypertension for the study cohort was lower than general population which may be the healthy worker effect. Obesity, alcohol use, and smoking rates however, were slightly higher in the study cohort. Reducing the prevalence of risk factors will require significant resources.

Structural Basis for the Activation of the Deubiquitinase Calypso by the Polycomb Protein ASX.

Ubiquitin C-terminal hydrolase deubiquitinase BAP1 is an essential tumor suppressor involved in cell growth control, DNA damage response, and transcriptional regulation. As part of the Polycomb repression machinery, BAP1 is activated by the deubiquitinase adaptor domain of ASXL1 mediating gene repression by cleaving ubiquitin (Ub) from histone H2A in nucleosomes. The molecular mechanism of BAP1 activation by ASXL1 remains elusive, as no structures are available for either BAP1 or ASXL1. Here, we present the crystal structure of the BAP1 ortholog from Drosophila melanogaster, named Calypso, bound to its activator, ASX, homolog of ASXL1. Based on comparative structural and functional analysis, we propose a model for Ub binding by Calypso/ASX, uncover decisive structural elements responsible for ASX-mediated Calypso activation, and characterize the interaction with ubiquitinated nucleosomes. Our results give molecular insight into Calypso function and its regulation by ASX and provide the opportunity for the rational design of mechanism-based therapeutics to treat human BAP1/ASXL1-related tumors.

Structure and Function of Roundabout Receptors.

The creation of complex neuronal networks relies on ligand-receptor interactions that mediate attraction or repulsion towards specific targets. Roundabouts comprise a family of single-pass transmembrane receptors facilitating this process upon interaction with the soluble extracellular ligand Slit protein family emanating from the midline. Due to the complexity and flexible nature of Robo receptors , their overall structure has remained elusive until now. Recent structural studies of the Robo 1 and Robo 2 ectodomains have provided the basis for a better understanding of their signalling mechanism. These structures reveal how Robo receptors adopt an auto-inhibited conformation on the cell surface that can be further stabilised by cis and/or trans oligmerisation arrays. Upon Slit -N binding Robo receptors must undergo a conformational change for Ig4 mediated dimerisation and signaling, probably via endocytosis. Furthermore, it's become clear that Robo receptors do not only act alone, but as large and more complex cell surface receptor assemblies to manifest directional and growth effects in a concerted fashion. These context dependent assemblies provide a mechanism to fine tune attractive and repulsive signals in a combinatorial manner required during neuronal development. While a mechanistic understanding of Slit mediated Robo signaling has advanced significantly further structural studies on larger assemblies are required for the design of new experiments to elucidate their role in cell surface receptor complexes. These will be necessary to understand the role of Slit -Robo signaling in neurogenesis, angiogenesis, organ development and cancer progression. In this chapter, we provide a review of the current knowledge in the field with a particular focus on the Roundabout receptor family.

Methylation of Structured RNA by the m6A Writer METTL16 Is Essential for Mouse Embryonic Development.

Internal modification of RNAs with N6-methyladenosine (m6A) is a highly conserved means of gene expression control. While the METTL3/METTL14 heterodimer adds this mark on thousands of transcripts in a single-stranded context, the substrate requirements and physiological roles of the second m6A writer METTL16 remain unknown. Here we describe the crystal structure of human METTL16 to reveal a methyltransferase domain furnished with an extra N-terminal module, which together form a deep-cut groove that is essential for RNA binding. When presented with a random pool of RNAs, METTL16 selects for methylation-structured RNAs where the critical adenosine is present in a bulge. Mouse 16-cell embryos lacking Mettl16 display reduced mRNA levels of its methylation target, the SAM synthetase Mat2a. The consequence is massive transcriptome dysregulation in ∼64-cell blastocysts that are unfit for further development. This highlights the role of an m6A RNA methyltransferase in facilitating early development via regulation of SAM availability.

Robo1 Forms a Compact Dimer-of-Dimers Assembly.

Roundabout (Robo) receptors provide an essential repulsive cue in neuronal development following Slit ligand binding. This important signaling pathway can also be hijacked in numerous cancers, making Slit-Robo an attractive therapeutic target. However, little is known about how Slit binding mediates Robo activation. Here we present the crystal structure of Robo1 Ig1-4 and Robo1 Ig5, together with a negative stain electron microscopy reconstruction of the Robo1 ectodomain. These results show how the Robo1 ectodomain is arranged as compact dimers, mainly mediated by the central Ig domains, which can further interact in a "back-to-back" fashion to generate a tetrameric assembly. We also observed no change in Robo1 oligomerization upon interaction with the dimeric Slit2-N ligand using fluorescent imaging. Taken together with previous studies we propose that Slit2-N binding results in a conformational change of Robo1 to trigger cell signaling.

Asymmetric ring structure of Vps4 required for ESCRT-III disassembly.

The vacuolar protein sorting 4 AAA-ATPase (Vps4) recycles endosomal sorting complexes required for transport (ESCRT-III) polymers from cellular membranes. Here we present a 3.6-Å X-ray structure of ring-shaped Vps4 from Metallosphera sedula (MsVps4), seen as an asymmetric pseudohexamer. Conserved key interface residues are shown to be important for MsVps4 assembly, ATPase activity in vitro, ESCRT-III disassembly in vitro and HIV-1 budding. ADP binding leads to conformational changes within the protomer, which might propagate within the ring structure. All ATP-binding sites are accessible and the pseudohexamer binds six ATP with micromolar affinity in vitro. In contrast, ADP occupies one high-affinity and five low-affinity binding sites in vitro, consistent with conformational asymmetry induced on ATP hydrolysis. The structure represents a snapshot of an assembled Vps4 conformation and provides insight into the molecular motions the ring structure undergoes in a concerted action to couple ATP hydrolysis to ESCRT-III substrate disassembly.

Mammalian translation elongation factor eEF1A2: X-ray structure and new features of GDP/GTP exchange mechanism in higher eukaryotes.

Eukaryotic elongation factor eEF1A transits between the GTP- and GDP-bound conformations during the ribosomal polypeptide chain elongation. eEF1A*GTP establishes a complex with the aminoacyl-tRNA in the A site of the 80S ribosome. Correct codon-anticodon recognition triggers GTP hydrolysis, with subsequent dissociation of eEF1A*GDP from the ribosome. The structures of both the 'GTP'- and 'GDP'-bound conformations of eEF1A are unknown. Thus, the eEF1A-related ribosomal mechanisms were anticipated only by analogy with the bacterial homolog EF-Tu. Here, we report the first crystal structure of the mammalian eEF1A2*GDP complex which indicates major differences in the organization of the nucleotide-binding domain and intramolecular movements of eEF1A compared to EF-Tu. Our results explain the nucleotide exchange mechanism in the mammalian eEF1A and suggest that the first step of eEF1A*GDP dissociation from the 80S ribosome is the rotation of the nucleotide-binding domain observed after GTP hydrolysis.

Structural basis for the activation of innate immune pattern-recognition receptor RIG-I by viral RNA.

RIG-I is a key innate immune pattern-recognition receptor that triggers interferon expression upon detection of intracellular 5'triphosphate double-stranded RNA (5'ppp-dsRNA) of viral origin. RIG-I comprises N-terminal caspase activation and recruitment domains (CARDs), a DECH helicase, and a C-terminal domain (CTD). We present crystal structures of the ligand-free, autorepressed, and RNA-bound, activated states of RIG-I. Inactive RIG-I has an open conformation with the CARDs sequestered by a helical domain inserted between the two helicase moieties. ATP and dsRNA binding induce a major rearrangement to a closed conformation in which the helicase and CTD bind the blunt end 5'ppp-dsRNA with perfect complementarity but incompatibly with continued CARD binding. We propose that after initial binding of 5'ppp-dsRNA to the flexibly linked CTD, co-operative tight binding of ATP and RNA to the helicase domain liberates the CARDs for downstream signaling. These findings significantly advance our molecular understanding of the activation of innate immune signaling helicases.

Structure of SRP14 from the Schizosaccharomyces pombe signal recognition particle.

The signal recognition particle (SRP) Alu domain has been implicated in translation elongation arrest in yeasts and mammals. Fission yeast SRP RNA is similar to that of mammals, but has a minimal Alu-domain RNA lacking two stem-loops. The mammalian Alu-domain proteins SRP9 and SRP14 bind their cognate Alu RNA as a heterodimer. However, in yeasts, notably Saccharomyces cerevisiae, SRP14 is thought to bind Alu RNA as a homodimer, the SRP9 protein being replaced by SRP21, the function of which is not yet clear. Structural characterization of the Schizosaccharomyces pombe Alu domain may thus help to identify the critical features required for elongation arrest. Here, the crystal structure of the SRP14 subunit of S. pombe SRP (SpSRP14) which crystallizes as a homodimer, is presented. Comparison of the SpSRP14 homodimer with the known structure of human SRP9/14 in complex with Alu RNA suggests that many of the protein-RNA contacts centred on the conserved U-turn motif are likely to be conserved in fission yeast. Initial attempts to solve the structure using traditional selenomethionine SAD labelling failed. However, two As atoms originating from the cacodylate buffer were found to make cysteine adducts and strongly contributed to the anomalous substructure. These adducts were highly radiation-sensitive and this property was exploited using the RIP (radiation-damage-induced phasing) method. The combination of SAD and RIP phases yielded an interpretable electron-density map. This example will be of general interest to crystallographers attempting de novo phasing from crystals grown in cacodylate buffer.