Könneke, M. et al. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437, 543–546 (2005).
Hutchins, D. A. & Capone, D. G. The marine nitrogen cycle: new developments and global change. Nat. Rev. Microbiol. 20, 401–414 (2022).
Karner, M. B., DeLong, E. F. & Karl, D. M. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409, 507–510 (2001).
Könneke, M. et al. Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation. Proc. Natl Acad. Sci. USA 111, 8239–8244 (2014).
Kraft, B. et al. Oxygen and nitrogen production by an ammonia-oxidizing archaeon. Science 375, 97–100 (2022).
Wan, X. S. et al. Ambient nitrate switches the ammonium consumption pathway in the euphotic ocean. Nat. Commun. 9, 915 (2018).
Martens-Habbena, W., Berube, P. M., Urakawa, H., de la Torre, J. R. & Stahl, D. A. Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature 461, 976–979 (2009).
Urakawa, H., Martens-Habbena, W. & Stahl, D. A. in Nitrification 115–155 (John Wiley & Sons, 2011).
Qin, W. et al. Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota. Int. J. Syst. Evol. Microbiol. 67, 5067–5079 (2017).
Bharat, T. A. M., von Kügelgen, A. & Alva, V. Molecular logic of prokaryotic surface layer structures. Trends Microbiol. 29, 405–415 (2021).
Albers, S. V. & Meyer, B. H. The archaeal cell envelope. Nat. Rev. Microbiol. 9, 414–426 (2011).
Li, P. N. et al. Nutrient transport suggests an evolutionary basis for charged archaeal surface layer proteins. ISME J. 12, 2389–2402 (2018).
Li, P. N., Herrmann, J., Wakatsuki, S. & van den Bedem, H. Transport properties of nanoporous, chemically forced biological lattices. J. Phys. Chem. B 123, 10331–10342 (2019).
Nakagawa, T. & Stahl, D. A. Transcriptional response of the archaeal ammonia oxidizer Nitrosopumilus maritimus to low and environmentally relevant ammonia concentrations. Appl. Environ. Microbiol. 79, 6911–6916 (2013).
Qin, W. et al. Stress response of a marine ammonia-oxidizing archaeon informs physiological status of environmental populations. ISME J. 12, 508–519 (2018).
von Kügelgen, A. et al. In Situ structure of an intact lipopolysaccharide-bound bacterial surface layer. Cell 180, 348–358 (2020).
Bharat, T. A. M. et al. Structure of the hexagonal surface layer on Caulobacter crescentus cells. Nat. Microbiol. 2, 17059 (2017).
von Kügelgen, A., Alva, V. & Bharat, T. A. M. Complete atomic structure of a native archaeal cell surface. Cell Rep. 37, 110052 (2021).
Zivanov, J. et al. A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0. eLife 11, e83724 (2022).
Jarrell, K. F. et al. N-linked glycosylation in Archaea: a structural, functional, and genetic analysis. Microbiol. Mol. Biol. Rev. 78, 304–341 (2014).
Herdman, M. et al. High-resolution mapping of metal ions reveals principles of surface layer assembly in Caulobacter crescentus cells. Structure 30, 215–228 (2022).
Baranova, E. et al. SbsB structure and lattice reconstruction unveil Ca2+ triggered S-layer assembly. Nature 487, 119–122 (2012).
von Kügelgen, A. et al. Interdigitated immunoglobulin arrays form the hyperstable surface layer of the extremophilic bacterium Deinococcus radiodurans. Proc. Natl Acad. Sci. USA 120, e2215808120 (2023).
Gambelli, L. et al. Structure of the two-component S-layer of the archaeon Sulfolobus acidocaldarius. eLife 13, e84617 (2024).
Gambelli, L. et al. Architecture and modular assembly of Sulfolobus S-layers revealed by electron cryotomography. Proc. Natl Acad. Sci. USA 116, 25278–25286 (2019).
Fioravanti, A. et al. Structure of S-layer protein Sap reveals a mechanism for therapeutic intervention in anthrax. Nat. Microbiol. 4, 1805–1814 (2019).
Bharat, T. A. M., Tocheva, E. I. & Alva, V. The cell envelope architecture of Deinococcus: HPI forms the S-layer and SlpA tethers the outer membrane to peptidoglycan. Proc. Natl Acad. Sci. USA 120, e2305338120 (2023).
Kim, J.-G. et al. Spindle-shaped viruses infect marine ammonia-oxidizing thaumarchaea. Proc. Natl Acad. Sci. USA 116, 15645–15650 (2019).
Song, W. et al. PyLipID: a Python package for analysis of protein-lipid interactions from molecular dynamics simulations. J. Chem. Theory Comput. 18, 1188–1201 (2022).
Xue, L. et al. Visualizing translation dynamics at atomic detail inside a bacterial cell. Nature 610, 205–211 (2022).
Tegunov, D., Xue, L., Dienemann, C., Cramer, P. & Mahamid, J. Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells. Nat. Methods 18, 186–193 (2021).
Hollocher, T. C., Tate, M. E. & Nicholas, D. J. Oxidation of ammonia by Nitrosomonas europaea. Definite 18O-tracer evidence that hydroxylamine formation involves a monooxygenase. J. Biol. Chem. 256, 10834–10836 (1981).
Hodgskiss, L. H. et al. Unexpected complexity of the ammonia monooxygenase in archaea. ISME J. 17, 588–599 (2023).
Vajrala, N. et al. Hydroxylamine as an intermediate in ammonia oxidation by globally abundant marine archaea. Proc. Natl Acad. Sci. USA 110, 1006–1011 (2013).
Leininger, S. et al. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442, 806–809 (2006).
Buchholz, T.-O. et al. in Methods in Cell Biology Vol. 152 (eds Müller-Reichert, T. & Pigino, G.) 277–289 (Academic, 2019).
Buchholz, T.-O., Jordan, M., Pigino, G. & Jug, F. Cryo-CARE: Content-aware image restoration for cryo-transmission electron microscopy data. In Proc. 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019) 502–506 (IEEE, 2019).
Sanchez-Garcia, R. et al. DeepEMhancer: a deep learning solution for cryo-EM volume post-processing. Commun. Biol. 4, 874 (2021).
Schouten, S. et al. Intact membrane lipids of “Candidatus Nitrosopumilus maritimus,” a cultivated representative of the cosmopolitan mesophilic group I Crenarchaeota. Appl. Environ. Microbiol. 74, 2433–2440 (2008).
Leavitt, W. et al. Archaeal lipid hydrogen isotopes in a marine thaumarchaeon. Earth Space Sci. Open Arch. https://doi.org/10.1002/essoar.10512169.1 (2022).
von Kügelgen, A., van Dorst, S., Alva, V. & Bharat, T. A. M. A multidomain connector links the outer membrane and cell wall in phylogenetically deep-branching bacteria. Proc. Natl Acad. Sci. USA 119, e2203156119 (2022).
Wan, W. et al. Structure and assembly of the Ebola virus nucleocapsid. Nature 551, 394–397 (2017).
Hagen, W. J. H., Wan, W. & Briggs, J. A. G. Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging. J. Struct. Biol. 197, 191–198 (2017).
Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36–51 (2005).
Kremer, J. R., Mastronarde, D. N. & McIntosh, J. R. Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116, 71–76 (1996).
Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).
Agulleiro, J. I. & Fernandez, J. J. Tomo3D 2.0—exploitation of advanced vector extensions (AVX) for 3D reconstruction. J. Struct. Biol. 189, 147–152 (2015).
Bharat, T. A. M. et al. Cryo-electron tomography of Marburg virus particles and their morphogenesis within infected cells. PLoS Biol. 9, e1001196 (2011).
Turoňová, B., Schur, F. K. M., Wan, W. & Briggs, J. A. G. Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4 Å. J. Struct. Biol. 199, 187–195 (2017).
Ilca, S. L. et al. Multiple liquid crystalline geometries of highly compacted nucleic acid in a dsRNA virus. Nature 570, 252–256 (2019).
Abrishami, V. et al. Localized reconstruction in Scipion expedites the analysis of symmetry mismatches in cryo-EM data. Prog. Biophys. Mol. Biol. 160, 43–52 (2021).
Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).
Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018).
Bepler, T. et al. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nat. Methods 16, 1153–1160 (2019).
Zivanov, J., Nakane, T. & Scheres, S. H. W. Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in RELION-3.1. IUCrJ 7, 253–267 (2020).
Scheres, S. H. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012).
Tan, Y. Z. et al. Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nat. Methods 14, 793–796 (2017).
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010).
Murshudov, G. N. et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D 67, 355–367 (2011).
Burnley, T., Palmer, C. M. & Winn, M. Recent developments in the CCP-EM software suite. Acta Crystallogr. D 73, 469–477 (2017).
Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D 75, 861–877 (2019).
Yamashita, K., Palmer, C. M., Burnley, T. & Murshudov, G. N. Cryo-EM single-particle structure refinement and map calculation using Servalcat. Acta Crystallogr. D 77, 1282–1291 (2021).
Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).
The PyMOL molecular graphics system v.2.0 (Schrödinger, 2015).
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
Qu, K. et al. Structure and architecture of immature and mature murine leukemia virus capsids. Proc. Natl Acad. Sci. USA 115, E11751–E11760 (2018).
Ermel, U. H., Arghittu, S. M. & Frangakis, A. S. ArtiaX: an electron tomography toolbox for the interactive handling of sub-tomograms in UCSF ChimeraX. Protein Sci. 31, e4472 (2022).
Zimmermann, L. et al. A completely reimplemented MPI bioinformatics Toolkit with a new HHpred server at its core. J. Mol. Biol. 430, 2237–2243 (2018).
Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinform. 10, 421 (2009).
Steinegger, M. et al. HH-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinform. 20, 473 (2019).
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
Teufel, F. et al. SignalP 6.0 predicts all five types of signal peptides using protein language models. Nat. Biotechnol. 40, 1023–1025 (2022).
Rice, P., Longden, I. & Bleasby, A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 16, 276–277 (2000).
Frickey, T. & Lupas, A. CLANS: a Java application for visualizing protein families based on pairwise similarity. Bioinformatics 20, 3702–3704 (2004).
Kozlowski, L. P. IPC 2.0: prediction of isoelectric point and pKa dissociation constants. Nucleic Acids Res. 49, W285–W292 (2021).
