Membraneless channels sieve cations in ammonia-oxidizing marine archaea

Nitrosopumilus maritimus is an ammonia-oxidizing archaeon that is crucial to the global nitrogen cycle1, 2. A critical step for nitrogen oxidation is the entrapment of ammonium ions from a dilute marine environment at the cell surface and their subsequent channelling to the cell membrane of N. maritimus. Here we elucidate the structure of the molecular machinery responsible for this process, comprising the surface layer (S-layer), using electron cryotomography and subtomogram averaging from cells. We supplemented our in situ structure of the ammonium-binding S-layer array with a single-particle electron cryomicroscopy structure, revealing detailed features of this immunoglobulin-rich and glycan-decorated S-layer. Biochemical analyses showed strong ammonium binding by the cell surface, which was lost after S-layer disassembly. Sensitive bioinformatic analyses identified similar S-layers in many ammonia-oxidizing archaea, with conserved sequence and structural characteristics. Moreover, molecular simulations and structure determination of ammonium-enriched specimens enabled us to examine the cation-binding properties of the S-layer, revealing how it concentrates ammonium ions on its cell-facing side, effectively acting as a multichannel sieve on the cell membrane. This in situ structural study illuminates the biogeochemically essential process of ammonium binding and channelling, common to many marine microorganisms that are fundamental to the nitrogen cycle

Vaccine breakthrough hypoxemic COVID-19 pneumonia in patients with auto-Abs neutralizing type I IFNs

Life-threatening `breakthrough' cases of critical COVID-19 are attributed to poor or waning antibody response to the SARS- CoV-2 vaccine in individuals already at risk. Pre-existing autoantibodies (auto-Abs) neutralizing type I IFNs underlie at least 15% of critical COVID-19 pneumonia cases in unvaccinated individuals; however, their contribution to hypoxemic breakthrough cases in vaccinated people remains unknown. Here, we studied a cohort of 48 individuals ( age 20-86 years) who received 2 doses of an mRNA vaccine and developed a breakthrough infection with hypoxemic COVID-19 pneumonia 2 weeks to 4 months later. Antibody levels to the vaccine, neutralization of the virus, and auto- Abs to type I IFNs were measured in the plasma. Forty-two individuals had no known deficiency of B cell immunity and a normal antibody response to the vaccine. Among them, ten (24%) had auto-Abs neutralizing type I IFNs (aged 43-86 years). Eight of these ten patients had auto-Abs neutralizing both IFN-a2 and IFN-., while two neutralized IFN-omega only. No patient neutralized IFN-ss. Seven neutralized 10 ng/mL of type I IFNs, and three 100 pg/mL only. Seven patients neutralized SARS-CoV-2 D614G and the Delta variant (B.1.617.2) efficiently, while one patient neutralized Delta slightly less efficiently. Two of the three patients neutralizing only 100 pg/mL of type I IFNs neutralized both D61G and Delta less efficiently. Despite two mRNA vaccine inoculations and the presence of circulating antibodies capable of neutralizing SARS-CoV-2, auto-Abs neutralizing type I IFNs may underlie a significant proportion of hypoxemic COVID-19 pneumonia cases, highlighting the importance of this particularly vulnerable population

Membraneless channels sieve cations in ammonia-oxidizing marine archaea.

Acknowledgements: This work was supported by the Medical Research Council, as part of UK Research and Innovation (programme MC_UP_1201/31 to T.A.M.B., U105184326 to J.L.). T.A.M.B. thanks the Human Frontier Science Program (grant RGY0074/2021), the Vallee Research Foundation, the European Molecular Biology Organization, the Leverhulme Trust and the Lister Institute for Preventative Medicine for support; V.A. thanks A. Lupas for continued support and the Human Frontier Science Program (grant RGY0074/2021); C.K.C. thanks P. Zhang and M. S. P. Sansom for their support as well as funding through the ERC AdG Program (grant 101021133) and a faculty start-up package from the University of Missouri-Columbia Department of Physics. We thank F. Elling and A. Pearson for the gift of a running N. maritimus cell culture; R. Rachel, S. H. W. Scheres and J. Zivanov for advice; and T. Darling, J. Grimmett, I. Clayson and J. J. E. Caesar for help with high-performance computing. One dataset for cryo-ET was acquired at the cryo-electron microscopy platform of the European Molecular Biology Laboratory (EMBL) in Heidelberg. This work was partly supported by institutional funds of the Max Planck Society; iNEXT, project number 653706, funded by the Horizon 2020 program of the European Union; and the MRC Laboratory of Molecular Biology Electron Microscopy Facility and Central Oxford Structural Molecular Imaging Centre (COSMIC). Simulations were performed on computational resources provided by HECBioSim, the UK High End Computing Consortium for Biomolecular Simulation, which is supported by the EPSRC (EP/L000253/1), as well as by the Research Computing Support Services division at the University of Missouri-Columbia, which is supported in part by the National Science Foundation (grant CNS-14229294). For the purpose of open access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright license to any Author Accepted Manuscript version arising.Nitrosopumilus maritimus is an ammonia-oxidizing archaeon that is crucial to the global nitrogen cycle1,2. A critical step for nitrogen oxidation is the entrapment of ammonium ions from a dilute marine environment at the cell surface and their subsequent channelling to the cell membrane of N. maritimus. Here we elucidate the structure of the molecular machinery responsible for this process, comprising the surface layer (S-layer), using electron cryotomography and subtomogram averaging from cells. We supplemented our in situ structure of the ammonium-binding S-layer array with a single-particle electron cryomicroscopy structure, revealing detailed features of this immunoglobulin-rich and glycan-decorated S-layer. Biochemical analyses showed strong ammonium binding by the cell surface, which was lost after S-layer disassembly. Sensitive bioinformatic analyses identified similar S-layers in many ammonia-oxidizing archaea, with conserved sequence and structural characteristics. Moreover, molecular simulations and structure determination of ammonium-enriched specimens enabled us to examine the cation-binding properties of the S-layer, revealing how it concentrates ammonium ions on its cell-facing side, effectively acting as a multichannel sieve on the cell membrane. This in situ structural study illuminates the biogeochemically essential process of ammonium binding and channelling, common to many marine microorganisms that are fundamental to the nitrogen cycle

Membraneless channels sieve cations in ammonia-oxidizing marine archaea.

Acknowledgements: This work was supported by the Medical Research Council, as part of UK Research and Innovation (programme MC_UP_1201/31 to T.A.M.B., U105184326 to J.L.). T.A.M.B. thanks the Human Frontier Science Program (grant RGY0074/2021), the Vallee Research Foundation, the European Molecular Biology Organization, the Leverhulme Trust and the Lister Institute for Preventative Medicine for support; V.A. thanks A. Lupas for continued support and the Human Frontier Science Program (grant RGY0074/2021); C.K.C. thanks P. Zhang and M. S. P. Sansom for their support as well as funding through the ERC AdG Program (grant 101021133) and a faculty start-up package from the University of Missouri-Columbia Department of Physics. We thank F. Elling and A. Pearson for the gift of a running N. maritimus cell culture; R. Rachel, S. H. W. Scheres and J. Zivanov for advice; and T. Darling, J. Grimmett, I. Clayson and J. J. E. Caesar for help with high-performance computing. One dataset for cryo-ET was acquired at the cryo-electron microscopy platform of the European Molecular Biology Laboratory (EMBL) in Heidelberg. This work was partly supported by institutional funds of the Max Planck Society; iNEXT, project number 653706, funded by the Horizon 2020 program of the European Union; and the MRC Laboratory of Molecular Biology Electron Microscopy Facility and Central Oxford Structural Molecular Imaging Centre (COSMIC). Simulations were performed on computational resources provided by HECBioSim, the UK High End Computing Consortium for Biomolecular Simulation, which is supported by the EPSRC (EP/L000253/1), as well as by the Research Computing Support Services division at the University of Missouri-Columbia, which is supported in part by the National Science Foundation (grant CNS-14229294). For the purpose of open access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright license to any Author Accepted Manuscript version arising.Nitrosopumilus maritimus is an ammonia-oxidizing archaeon that is crucial to the global nitrogen cycle1,2. A critical step for nitrogen oxidation is the entrapment of ammonium ions from a dilute marine environment at the cell surface and their subsequent channelling to the cell membrane of N. maritimus. Here we elucidate the structure of the molecular machinery responsible for this process, comprising the surface layer (S-layer), using electron cryotomography and subtomogram averaging from cells. We supplemented our in situ structure of the ammonium-binding S-layer array with a single-particle electron cryomicroscopy structure, revealing detailed features of this immunoglobulin-rich and glycan-decorated S-layer. Biochemical analyses showed strong ammonium binding by the cell surface, which was lost after S-layer disassembly. Sensitive bioinformatic analyses identified similar S-layers in many ammonia-oxidizing archaea, with conserved sequence and structural characteristics. Moreover, molecular simulations and structure determination of ammonium-enriched specimens enabled us to examine the cation-binding properties of the S-layer, revealing how it concentrates ammonium ions on its cell-facing side, effectively acting as a multichannel sieve on the cell membrane. This in situ structural study illuminates the biogeochemically essential process of ammonium binding and channelling, common to many marine microorganisms that are fundamental to the nitrogen cycle

First detection of NH<SUB>3</SUB> (1<SUB>0</SUB> -> 0<SUB>0</SUB>) from a low mass cloud core. On the low ammonia abundance of the rho Oph A core

International audienc

First detection of NH<SUB>3</SUB> (1<SUB>0</SUB> -> 0<SUB>0</SUB>) from a low mass cloud core. On the low ammonia abundance of the rho Oph A core

International audienc

Highlights from the first year of Odin observations

International audienc

Molecular oxygen in the rho Ophiuchi cloud

International audienceContext: Molecular oxygen, O2, has been expected historically to be an abundant component of the chemical species in molecular clouds and, as such, an important coolant of the dense interstellar medium. However, a number of attempts from both ground and from space have failed to detect O2 emission. Aims: The work described here uses heterodyne spectroscopy from space to search for molecular oxygen in the interstellar medium. Methods: The Odin satellite carries a 1.1 m sub-millimeter dish and a dedicated 119 GHz receiver for the ground state line of O2. Starting in 2002, the star forming molecular cloud core rho {Oph A} was observed with Odin for 34 days during several observing runs. Results: We detect a spectral line at v_LSR =+3.5 km s-1 with Delta v_FWHM=1.5 km s-1, parameters which are also common to other species associated with rho {Oph A}. This feature is identified as the O2 (NJ = 11 - 1_0) transition at 118 750.343 MHz. Conclusions: The abundance of molecular oxygen, relative to H{2} , is 5 × 10-8 averaged over the Odin beam. This abundance is consistently lower than previously reported upper limits

Molecular oxygen in the rho Ophiuchi cloud

International audienceContext: Molecular oxygen, O2, has been expected historically to be an abundant component of the chemical species in molecular clouds and, as such, an important coolant of the dense interstellar medium. However, a number of attempts from both ground and from space have failed to detect O2 emission. Aims: The work described here uses heterodyne spectroscopy from space to search for molecular oxygen in the interstellar medium. Methods: The Odin satellite carries a 1.1 m sub-millimeter dish and a dedicated 119 GHz receiver for the ground state line of O2. Starting in 2002, the star forming molecular cloud core rho {Oph A} was observed with Odin for 34 days during several observing runs. Results: We detect a spectral line at v_LSR =+3.5 km s-1 with Delta v_FWHM=1.5 km s-1, parameters which are also common to other species associated with rho {Oph A}. This feature is identified as the O2 (NJ = 11 - 1_0) transition at 118 750.343 MHz. Conclusions: The abundance of molecular oxygen, relative to H{2} , is 5 × 10-8 averaged over the Odin beam. This abundance is consistently lower than previously reported upper limits

Highlights from the first year of Odin observations

International audienc