SigmaR1 shapes rough endoplasmic reticulum membrane sheets.

Rough endoplasmic reticulum (ER) sheets are a fundamental domain of the ER and the gateway into the secretory pathway. Although reticulon proteins stabilize high-curvature ER tubules, it is unclear whether other proteins scaffold the flat membranes of rough ER sheets. Through a proteomics screen using ER sheet-localized RNA-binding proteins as bait, we identify the sigma-1 receptor (SigmaR1) as an ER sheet-shaping factor. High-resolution live cell imaging and electron tomography assign SigmaR1 as an ER sheet-localized factor whose levels determine the amount of rough ER sheets in cells. Structure-guided mutagenesis and in vitro reconstitution on giant unilamellar vesicles further support a mechanism whereby SigmaR1 oligomers use their extended arrays of amphipathic helices to bind and flatten the lumenal leaflet of ER membranes to oppose membrane curvature and stabilize rough ER sheets.

Mechanism and cellular function of direct membrane binding by the ESCRT and ERES-associated Ca2+-sensor ALG-2.

Apoptosis linked Gene-2 (ALG-2) is a multifunctional intracellular Ca2+ sensor and the archetypal member of the penta-EF hand protein family. ALG-2 functions in the repair of damage to both the plasma and lysosome membranes and in COPII-dependent budding at endoplasmic reticulum exit sites (ERES). In the presence of Ca2+, ALG-2 binds to ESCRT-I and ALIX in membrane repair and to SEC31A at ERES. ALG-2 also binds directly to acidic membranes in the presence of Ca2+ by a combination of electrostatic and hydrophobic interactions. By combining giant unilamellar vesicle-based experiments and molecular dynamics simulations, we show that charge-reversed mutants of ALG-2 at these locations disrupt membrane recruitment. ALG-2 membrane binding mutants have reduced or abrogated ERES localization in response to Thapsigargin-induced Ca2+ release but still localize to lysosomes following lysosomal Ca2+ release. In vitro reconstitution shows that the ALG-2 membrane-binding defect can be rescued by binding to ESCRT-I. These data thus reveal the nature of direct Ca2+-dependent membrane binding and its interplay with Ca2+-dependent protein binding in the cellular functions of ALG-2.

Mechanism and cellular function of direct membrane binding by the ESCRT and ERES-associated Ca2+-sensor ALG-2.

Apoptosis Linked Gene-2 (ALG-2) is a multifunctional intracellular Ca2+ sensor and the archetypal member of the penta-EF hand protein family. ALG-2 functions in the repair of damage to both the plasma and lysosome membranes and in COPII-dependent budding at endoplasmic reticulum exit sites (ERES). In the presence of Ca2+, ALG-2 binds to ESCRT-I and ALIX in membrane repair and to SEC31A at ERES. ALG-2 also binds directly to acidic membranes in the presence of Ca2+ by a combination of electrostatic and hydrophobic interactions. By combining GUV-based experiments and molecular dynamics simulations, we show that charge-reversed mutants of ALG-2 at these locations disrupt membrane recruitment. ALG-2 membrane binding mutants have reduced or abrogated ERES localization in response to Thapsigargin-induced Ca2+ release but still localize to lysosomes following lysosomal Ca2+ release. In vitro reconstitution shows that the ALG-2 membrane-binding defect can be rescued by binding to ESCRT-I. These data thus reveal the nature of direct Ca2+-dependent membrane binding and its interplay with Ca2+-dependent protein binding in the cellular functions of ALG-2.

Adapted Kaizen: Multi-Organizational Complex Process Redesign for Adapting Clinical Guidelines for the Digital Age.

The need for a method to examine complex, multidisciplinary processes involving many diverse organizations initially led multiple US federal agencies to adopt the traditional Kaizen, a Lean process improvement method typically used within a single organization, to encompass multiple organizations each with its own leadership and priorities. First, the Centers for Medicare and Medicaid Services and the Office of the National Coordinator for Health Information Technology adapted Kaizen to federal agency processes for the development of electronic clinical quality measures. Later, the Centers for Disease Control and Prevention (CDC) further modified this adapted Kaizen during its Adapting Clinical Guidelines for the Digital Age (ACG) initiative, which aimed to improve the broader scope of guideline development and implementation. This is a methods article to document the adapted Kaizen method for future use in similar complex processes, illustrating how to apply the adapted Kaizen through CDC's ACG initiative and showing the reach achieved by using the adapted Kaizen method. The adapted Kaizen includes pre-Kaizen planning, a Kaizen event, and post-Kaizen implementation that accommodate multidisciplinary and multi-organizational participation. ACG included 5 workgroups that each developed products to support their respective scope: Guideline Creation, Informatics Framework, Translation and Implementation, Communication and Dissemination, and Evaluation. Despite challenges gathering diverse perspectives and balancing the competing priorities of multiple organizations, the ACG participants produced interrelated standards, processes, and tools-further described in separate publications-that programs and partners have leveraged. Use of a siloed approach may not have supported the development and dissemination of these products.

Pressure pushes tRNALys3 into excited conformational states.

Conformational dynamics play essential roles in RNA function. However, detailed structural characterization of excited states of RNA remains challenging. Here, we apply high hydrostatic pressure (HP) to populate excited conformational states of tRNALys3, and structurally characterize them using a combination of HP 2D-NMR, HP-SAXS (HP-small-angle X-ray scattering), and computational modeling. HP-NMR revealed that pressure disrupts the interactions of the imino protons of the uridine and guanosine U-A and G-C base pairs of tRNALys3. HP-SAXS profiles showed a change in shape, but no change in overall extension of the transfer RNA (tRNA) at HP. Configurations extracted from computational ensemble modeling of HP-SAXS profiles were consistent with the NMR results, exhibiting significant disruptions to the acceptor stem, the anticodon stem, and the D-stem regions at HP. We propose that initiation of reverse transcription of HIV RNA could make use of one or more of these excited states.

In vitro reconstitution of calcium-dependent recruitment of the human ESCRT machinery in lysosomal membrane repair.

The endosomal sorting complex required for transport (ESCRT) machinery is centrally involved in the repair of damage to both the plasma and lysosome membranes. ESCRT recruitment to sites of damage occurs on a fast time scale, and Ca2+ has been proposed to play a key signaling role in the process. Here, we show that the Ca2+-binding regulatory protein ALG-2 binds directly to negatively charged membranes in a Ca2+-dependent manner. Next, by monitoring the colocalization of ALIX with ALG-2 on negatively charged membranes, we show that ALG-2 recruits ALIX to the membrane. Furthermore, we show that ALIX recruitment to the membrane orchestrates the downstream assembly of late-acting CHMP4B, CHMP3, and CHMP2A subunits along with the AAA+ ATPase VPS4B. Finally, we show that ALG-2 can also recruit the ESCRT-III machinery to the membrane via the canonical ESCRT-I/II pathway. Our reconstitution experiments delineate the minimal sets of components needed to assemble the entire membrane repair machinery and open an avenue for the mechanistic understanding of endolysosomal membrane repair.

Friction-driven membrane scission by the human ESCRT-III proteins CHMP1B and IST1.

The endosomal sorting complexes required for transport (ESCRT) system is an ancient and ubiquitous membrane scission machinery that catalyzes the budding and scission of membranes. ESCRT-mediated scission events, exemplified by those involved in the budding of HIV-1, are usually directed away from the cytosol ("reverse topology"), but they can also be directed toward the cytosol ("normal topology"). The ESCRT-III subunits CHMP1B and IST1 can coat and constrict positively curved membrane tubes, suggesting that these subunits could catalyze normal topology membrane severing. CHMP1B and IST1 bind and recruit the microtubule-severing AAA+ ATPase spastin, a close relative of VPS4, suggesting that spastin could have a VPS4-like role in normal-topology membrane scission. Here, we reconstituted the process in vitro using membrane nanotubes pulled from giant unilamellar vesicles using an optical trap in order to determine whether CHMP1B and IST1 are capable of membrane severing on their own or in concert with VPS4 or spastin. CHMP1B and IST1 copolymerize on membrane nanotubes, forming stable scaffolds that constrict the tubes, but do not, on their own, lead to scission. However, CHMP1B-IST1 scaffolded tubes were severed when an additional extensional force was applied, consistent with a friction-driven scission mechanism. We found that spastin colocalized with CHMP1B-enriched sites but did not disassemble the CHMP1B-IST1 coat from the membrane. VPS4 resolubilized CHMP1B and IST1 without leading to scission. These observations show that the CHMP1B-IST1 ESCRT-III combination is capable of severing membranes by a friction-driven mechanism that is independent of VPS4 and spastin.

Developing a User-Centered Digital Clinical Decision Support App for Evidence-Based Medication Recommendations for Type 2 Diabetes Mellitus: Prototype User Testing and Validation Study.

BACKGROUND: Closing the gap between care recommended by evidence-based guidelines and care delivered in practice is an ongoing challenge across systems and delivery models. Clinical decision support systems (CDSSs) are widely deployed to augment clinicians in their complex decision-making processes. Despite published success stories, the poor usability of many CDSSs has contributed to fragmented workflows and alert fatigue. OBJECTIVE: This study aimed to validate the application of a user-centered design (UCD) process in the development of a standards-based medication recommender for type 2 diabetes mellitus in a simulated setting. The prototype app was evaluated for effectiveness, efficiency, and user satisfaction. METHODS: We conducted interviews with 8 clinical leaders with 8 rounds of iterative user testing with 2-8 prescribers in each round to inform app development. With the resulting prototype app, we conducted a validation study with 43 participants. The participants were assigned to one of two groups and completed a 2-hour remote user testing session. Both groups reviewed mock patient facts and ordered diabetes medications for the patients. The Traditional group used a mock electronic health record (EHR) for the review in Period 1 and used the prototype app in Period 2, while the Tool group used the prototype app during both time periods. The perceived cognitive load associated with task performance during each period was assessed with the National Aeronautics and Space Administration Task Load Index. Participants also completed the System Usability Scale (SUS) questionnaire and Kano Survey. RESULTS: Average SUS scores from the questionnaire, taken at the end of 5 of the 8 user testing sessions, ranged from 68-86. The results of the validation study are as follows: percent adherence to evidence-based guidelines was greater with the use of the prototype app than with the EHR across time periods with the Traditional group (prototype app mean 96.2 vs EHR mean 72.0, P<.001) and between groups during Period 1 (Tool group mean 92.6 vs Traditional group mean 72.0, P<.001). Task completion times did not differ between groups (P=.23), but the Tool group completed medication ordering more quickly in Period 2 (Period 1 mean 130.7 seconds vs Period 2 mean 107.7 seconds, P<.001). Based on an adjusted α level owing to violation of the assumption of homogeneity of variance (Ps>.03), there was no effect on screens viewed and on perceived cognitive load (all Ps>.14). CONCLUSIONS: Through deployment of the UCD process, a point-of-care medication recommender app holds promise of improving adherence to evidence-based guidelines; in this case, those from the American Diabetes Association. Task-time performance suggests that with practice the T2DM app may support a more efficient ordering process for providers, and SUS scores indicate provider satisfaction with the app.

High-resolution view of HIV-1 reverse transcriptase initiation complexes and inhibition by NNRTI drugs.

Reverse transcription of the HIV-1 viral RNA genome (vRNA) is an integral step in virus replication. Upon viral entry, HIV-1 reverse transcriptase (RT) initiates from a host tRNALys3 primer bound to the vRNA genome and is the target of key antivirals, such as non-nucleoside reverse transcriptase inhibitors (NNRTIs). Initiation proceeds slowly with discrete pausing events along the vRNA template. Despite prior medium-resolution structural characterization of reverse transcriptase initiation complexes (RTICs), higher-resolution structures of the RTIC are needed to understand the molecular mechanisms that underlie initiation. Here we report cryo-EM structures of the core RTIC, RTIC-nevirapine, and RTIC-efavirenz complexes at 2.8, 3.1, and 2.9 Å, respectively. In combination with biochemical studies, these data suggest a basis for rapid dissociation kinetics of RT from the vRNA-tRNALys3 initiation complex and reveal a specific structural mechanism of nucleic acid conformational stabilization during initiation. Finally, our results show that NNRTIs inhibit the RTIC and exacerbate discrete pausing during early reverse transcription.

Case Report: Transmission of Dengue Virus from a Deceased Donor to a Kidney Transplant Recipient Previously Infected by Dengue Virus.

Since 2018, a dengue epidemic has been ongoing in the French overseas department of Reunion Island, in the Indian Ocean, with more than 25,000 serologically confirmed cases. Currently, three dengue serotypes have been identified in Réunion Island (DENV-1, DENV-2, and DENV-3) progressing in the form of epidemic outbreaks. This arbovirus is mainly transmitted by mosquitoes of the genus Aedes and may be responsible for serious clinical forms. To date, very few cases of kidney transplant-related dengue virus infection have been described. Here we report the first case of severe dengue virus infection related to kidney transplantation from a patient previously infected with dengue. Testing for dengue fever with PCR search in donor's urine may help complete the pretransplant assessment in areas where this disease occurs.

Co-infection in patients with hypoxemic pneumonia due to COVID-19 in Reunion Island.

ABSTRACT: This study aimed to evaluate the incidence of co-infection with different types of pathogens in patients with hypoxemic pneumonia due to coronavirus disease 2019 (COVID-19) in Reunion Island.This observational study using a prospectively collected database of hypoxemic pneumonia due to COVID-19 cases was conducted at Félix Guyon University Hospital in Reunion Island, France.Between 18 March 2020 and 15 April 2020, 156 patients were admitted to our hospital for COVID-19. A total of 36 patients had hypoxemic pneumonia (23.1%) due to COVID-19. Thirty of these cases (83.3%) were imported by travelers returning mainly from metropolitan France and Spain. Patients were screened for co-infection with other pathogens at admission: 31 (86.1%) by multiplex polymerase chain reaction (PCR) and 16 (44.4%) by cytobacteriological examination of sputum culture. Five patients (13.9%) were found to have co-infection: 1 with influenza virus A H1N1 (pdm09) associated with Branhamella catarrhalis, 1 with Streptococcus pneumoniae associated with Haemophilus influenzae, 1 with Human Coronavirus 229E, 1 with Rhinovirus, and 1 with methicillin-susceptible Staphylococcus aureus. Patients with co-infection had higher D-dimer levels than those without co-infection (1.36 [1.34-2.36] µg/mL vs 0.63 [0.51-1.12] µg/mL, P = .05).The incidence of co-infection in our cohort was higher than expected (13.9%). Three co-infections (with influenza virus A(H1N1) pdm09, Streptococcus pneumoniae, and Staphylococcus aureus) required specific treatment. Patients with hypoxemic pneumonia due to COVID-19 should be screened for co-infection using respiratory cultures or multiplex PCR. Whilst our study has a number of limitations, the results from our study suggest that in the absence of screening, patients should be commenced on treatment for co-infection in the presence of an elevated D-dimer.

A comprehensive strategy for the early treatment of COVID-19 with azithromycin/hydroxychloroquine and/or corticosteroids: Results of a retrospective observational study in the French overseas department of Réunion Island.

BACKGROUND: This study aimed to evaluate the prognosis of COVID-19 patients in Reunion Island, with a particular focus on the management of patients with hypoxemic pneumonia. METHODS: This retrospective observational study was conducted from 11 March to 17 April 2020 at the only hospital authorized to manage patients with COVID-19 in Reunion Island. RESULTS: Over the study period, 164 out of 398 patients (41.2%) infected with COVID-19 were admitted to Félix Guyon University Hospital. Of these, 36 (22%) developed hypoxemic pneumonia. Patients with hypoxemic pneumonia were aged 66 [56-77] years, 69% were male and 33% had hypertension. Ten patients (27.8%) were hospitalized in intensive care unit (ICU). Hydroxychloroquine/azithromycin treatment was associated with a lower ICU admission rate (P=0.008). None of the 6 patients treated with corticosteroids were hospitalized in ICU (P=0.16). There were no deaths at follow up (minimum 80 days). CONCLUSIONS: Despite the risk profile of COVID-19 patients with severe hypoxemic pneumonia, the mortality rate of the disease in Reunion Island was 0%. This may be due to the care bundle used in our hospital (early hospitalisation, treatment with hydroxychloroquine/azithromycin and/or corticosteroids, non-invasive respiratory support, etc).

Detection of Pulmonary Embolism in Returning Travelers with Hypoxemic Pneumonia due to COVID-19 in Reunion Island.

The aim of this study was to evaluate the occurrence of pulmonary embolism in returning travelers with hypoxemic pneumonia due to COVID-19. All returning travelers to Reunion Island with hypoxemic pneumonia due to COVID-19 underwent computed tomography pulmonary angiography (CTPA) and were included in the cohort. Thirty-five patients were returning travelers with hypoxemic pneumonia due to COVID-19 and had recently returned from one of the countries most affected by the COVID-19 outbreak (mainly from France and Comoros archipelago). Five patients (14.3%) were found to have pulmonary embolism and two (5.9%) were incidentally found to have deep vein thrombosis on CTPA. Patients with pulmonary embolism or deep vein thrombosis had higher D-dimer levels than those without pulmonary embolism or deep vein thrombosis (P = 0.04). Returning travelers with hypoxemic pneumonia due to COVID-19 should be systematically screened for pulmonary embolism.

Distinct Conformational States Underlie Pausing during Initiation of HIV-1 Reverse Transcription.

A hallmark of the initiation step of HIV-1 reverse transcription, in which viral RNA genome is converted into double-stranded DNA, is that it is slow and non-processive. Biochemical studies have identified specific sites along the viral RNA genomic template in which reverse transcriptase (RT) stalls. These stalling points, which occur after the addition of three and five template dNTPs, may serve as checkpoints to regulate the precise timing of HIV-1 reverse transcription following viral entry. Structural studies of reverse transcriptase initiation complexes (RTICs) have revealed unique conformations that may explain the slow rate of incorporation; however, questions remain about the temporal evolution of the complex and features that contribute to strong pausing during initiation. Here we present cryo-electron microscopy and single-molecule characterization of an RTIC after three rounds of dNTP incorporation (+3), the first major pausing point during reverse transcription initiation. Cryo-electron microscopy structures of a +3 extended RTIC reveal conformational heterogeneity within the RTIC core. Three distinct conformations were identified, two of which adopt unique, likely off-pathway, intermediates in the canonical polymerization cycle. Single-molecule Förster resonance energy transfer experiments confirm that the +3 RTIC is more structurally dynamic than earlier-stage RTICs. These alternative conformations were selectively disrupted through structure-guided point mutations to shift single-molecule Förster resonance energy transfer populations back toward the on-pathway conformation. Our results support the hypothesis that conformational heterogeneity within the HIV-1 RTIC during pausing serves as an additional means of regulating HIV-1 replication.

Relating Structure and Dynamics in RNA Biology.

Recent advances in structural biology methods have enabled a surge in the number of RNA and RNA-protein assembly structures available at atomic or near-atomic resolution. These complexes are often trapped in discrete conformational states that exist along a mechanistic pathway. Single-molecule fluorescence methods provide temporal resolution to elucidate the dynamic mechanisms of processes involving complex RNA and RNA-protein assemblies, but interpretation of such data often requires previous structural knowledge. Here we highlight how single-molecule tools can directly complement structural approaches for two processes--translation and reverse transcription-to provide a dynamic view of molecular function.

De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes.

Increasingly, cryo-electron microscopy (cryo-EM) is used to determine the structures of RNA-protein assemblies, but nearly all maps determined with this method have biologically important regions where the local resolution does not permit RNA coordinate tracing. To address these omissions, we present de novo ribonucleoprotein modeling in real space through assembly of fragments together with experimental density in Rosetta (DRRAFTER). We show that DRRAFTER recovers near-native models for a diverse benchmark set of RNA-protein complexes including the spliceosome, mitochondrial ribosome, and CRISPR-Cas9-sgRNA complexes; rigorous blind tests include yeast U1 snRNP and spliceosomal P complex maps. Additionally, to aid in model interpretation, we present a method for reliable in situ estimation of DRRAFTER model accuracy. Finally, we apply DRRAFTER to recently determined maps of telomerase, the HIV-1 reverse transcriptase initiation complex, and the packaged MS2 genome, demonstrating the acceleration of accurate model building in challenging cases.

Dynamic Interplay of RNA and Protein in the Human Immunodeficiency Virus-1 Reverse Transcription Initiation Complex.

The initiation of reverse transcription in human immunodeficiency virus-1 is a key early step in the virus replication cycle. During this process, the viral enzyme reverse transcriptase (RT) copies the single-stranded viral RNA (vRNA) genome into double-stranded DNA using human tRNALys3 as a primer for initiation. The tRNA primer and vRNA genome contain several complementary sequences that are important for regulating reverse transcription initiation kinetics. Using single-molecule Förster resonance energy transfer spectroscopy, we demonstrate that the vRNA-tRNA initiation complex is conformationally heterogeneous and dynamic in the absence of RT. As shown previously, nucleic acid-RT interaction is characterized by rapid dissociation constants. We show that extension of the vRNA-tRNA primer binding site helix from 18 base pairs to 22 base pairs stabilizes RT binding to the complex and that the tRNA 5' end has a role in modulating RT binding. RT occupancy on the complex stabilizes helix 1 formation and reduces global structural heterogeneity. The stabilization of helix 1 upon RT binding may serve to destabilize helix 2, the first pause site for RT during initiation, during later steps of reverse transcription initiation.

Architecture of an HIV-1 reverse transcriptase initiation complex.

Reverse transcription of the HIV-1 RNA genome into double-stranded DNA is a central step in viral infection 1 and a common target of antiretroviral drugs 2 . The reaction is catalysed by viral reverse transcriptase (RT)3,4 that is packaged in an infectious virion with two copies of viral genomic RNA 5 each bound to host lysine 3 transfer RNA (tRNALys3), which acts as a primer for initiation of reverse transcription6,7. Upon viral entry into cells, initiation is slow and non-processive compared to elongation8,9. Despite extensive efforts, the structural basis of RT function during initiation has remained a mystery. Here we use cryo-electron microscopy to determine a three-dimensional structure of an HIV-1 RT initiation complex. In our structure, RT is in an inactive polymerase conformation with open fingers and thumb and with the nucleic acid primer-template complex shifted away from the active site. The primer binding site (PBS) helix formed between tRNALys3 and HIV-1 RNA lies in the cleft of RT and is extended by additional pairing interactions. The 5' end of the tRNA refolds and stacks on the PBS to create a long helical structure, while the remaining viral RNA forms two helical stems positioned above the RT active site, with a linker that connects these helices to the RNase H region of the PBS. Our results illustrate how RNA structure in the initiation complex alters RT conformation to decrease activity, highlighting a potential target for drug action.

Heterogeneous structures formed by conserved RNA sequences within the HIV reverse transcription initiation site.

Reverse transcription is a key process in the early steps of HIV infection. This process initiates within a specific complex formed by the 5' UTR of the HIV genomic RNA (vRNA) and a host primer tRNALys3 Using nuclear magnetic resonance (NMR) spectroscopy and single-molecule fluorescence spectroscopy, we detect two distinct conformers adopted by the tRNA/vRNA initiation complex. We directly show that an interaction between the conserved 8-nucleotide viral RNA primer activation signal (PAS) and the primer tRNA occurs in one of these conformers. This intermolecular PAS interaction likely induces strain on a vRNA intramolecular helix, which must be broken for reverse transcription to initiate. We propose a mechanism by which this vRNA/tRNA conformer relieves the kinetic block formed by the vRNA intramolecular helix to initiate reverse transcription.