Archaea: Exploring surface structures

The surface layer of Sulfolobus acidocaldarius consists of a flexible but stable outer protein layer that interacts with an inner, membrane-bound protein.
  1. Bernhard Schuster  Is a corresponding author
  1. Institute of Synthetic Bioarchitectures, Department of Bionanosciences, University of Natural Resources and Life Sciences, Vienna, Austria

Archaea and bacteria have much in common: both are single-celled microorganisms, and neither has a nucleus – so they are both prokaryotes. Archaea are also found in all the niches inhabited by bacteria. However, archaea can also survive in extreme niches where bacteria cannot. Most archaea live in very cold conditions, but they can also live in hot springs, or near deep-sea vents where temperatures can exceed 100 degrees Celsius, or in the extremely high pressures found at the bottom of the ocean. Other archaea can survive in conditions that are extremely saline, alkaline or acidic (down to pH 0), and some can even thrive in petroleum deposits deep underground.

How can archaea survive in these environments? And how, in particular, can archaeal cells withstand the extremes of temperature, pressure, salinity and pH that they are subjected to? The cell envelope in a prokaryote includes a cell wall that provides structural integrity, and a membrane that encloses the cytoplasm of the cell. There are important differences in the constituents and construction of the cell wall in archaea and bacteria, but there are also similarities, notably the presence in almost all archaea, as well as many bacteria, of a two-dimensional lattice called a surface layer (Sleytr et al., 1988; Bharat et al., 2021). These layers are made of subunits called surface-layer proteins (SLPs), and unlike what happens in bacteria, the surface layer in archaea – with just a few exceptions – must interact with the cytoplasmic membrane (Albers and Meyer, 2011; Rodrigues-Oliveira et al., 2017). Moreover, prokaryotes must synthesize, translocate to the cell surface, and incorporate into the existing lattice at least 500 copies of each SLP every second to maintain the surface layer (Sleytr et al., 1999).

In some archaea the surface layer is made of two different SLPs, although only one of these need interact with the cytoplasmic membrane. However, there is much about two-component surface layers that we do not fully understand. Now, in eLife, Bertram Daum from the University of Exeter and co-workers – including Lavinia Gambelli as first author – report details of an in situ atomic model of a two-component surface layer that sheds new light on the dynamics and assembly of these structures (Gambelli et al., 2024). The study was performed with samples from Sulfolobus acidocaldarius, an archaeal species that lives in hot springs, and relied on a combination of experimental techniques – notably cryo electron microscopy and cryo electron tomography – and a software package called Alphafold2 that predicts protein structures.

The surface layer in S. acidocaldarius is made of two proteins: SlaA is a Y-shaped soluble protein rich in β-strands, while SlaB contains three consecutive β-sandwich domains and a membrane-bound coiled-coil domain at its C-terminus (Figure 1A and B). In previous work Gambelli et al. had shown that the unit cell of the surface layer was hexagonal and contained three dimers of SlaA and a trimer of SlaB (Figure 1C; Gambelli et al., 2019).

The structure of a two-component surface layer in the cell envelop of the archaeal species Sulfolobus acidocaldarius.

The surface layer of S. acidocaldarius is made of two glycosylated proteins: SlaA, which is extracellular-facing and is shown here as a monomer (A), and SlaB, which is intracellular-facing and is shown here as a trimer (B): the glycosylation is not shown for either protein. (C) Schematic extracellular view of the unit cell of the surface layer, which contains three SlaA dimers (with the six monomers shown in different shades of green) and the SlaB trimer (with the monomers shown in shades of grey). The SlaA dimers assemble around a central, hexagonal pore. This also gives rises to a ring of six triangular pores, three of which are occupied by the SlaB trimer. (The trimer occupies the pores between adjacent dimers, and not the pores within the dimers). (D) Schematic side view of one unit cell. The SlaA dimers and the SlaB trimer create a canopy-like framework that is roughly parallel to the cytoplasmic membrane (shown in brown). Each SlaA protein contains six domains: the four domains nearest the N-terminus form the outermost surface, which is called the outer zone (OZ), and the other two domains project towards the cytoplasmic membrane and form the inner zone (IZ). The N-terminus of each monomer in the SlaB trimer interacts with the SlaA lattice, while the transmembrane domain at the C-terminus of each monomer anchor the lattice to the cytoplasmic membrane. Scale bar: 5 nm.

Now they show that the SlaA dimers assemble into a sheet with a thickness of 9.5 nm, and that the individual proteins adopt an angle of about 28° with respect to the plane of the cytoplasmic membrane. This sheet is anchored to the cytoplasmic membrane by the SlaB trimers – which have their long axes perpendicular to the SlaA sheet– to create a canopy-like framework with an overall thickness of 35 nm (Figure 1D). One of the reasons why the SlaA sheet is robust is because the SlaA proteins have formed dimers. However, there is also some flexibility in the structure because two of the six domains in each SlaA protein – the two domains nearest the C-terminus – do not adopt fixed positions, and are thus free to move to some extent.

Surface layers have already shown potential for applications in biotechnology, medicine and environmental science, and an improved understanding of these structures could lead to further applications in fields as diverse as ultrafiltration membranes and biosensors (Pfeifer et al., 2021; Pfeifer et al., 2022; Douglas et al., 1986). These applications in the real world are a long way from the extreme environments in which archaea are often found.

References

Article and author information

Author details

  1. Bernhard Schuster

    Bernhard Schuster is in the Institute of Synthetic Bioarchitectures, Department of Bionanosciences, University of Natural Resources and Life Sciences Vienna, Vienna, Austria

    For correspondence
    bernhard.schuster@boku.ac.at
    Competing interests
    No competing interests declared
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2584-204X

Publication history

  1. Version of Record published: February 28, 2024 (version 1)

Copyright

© 2024, Schuster

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 215
    views
  • 27
    downloads
  • 0
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Bernhard Schuster
(2024)
Archaea: Exploring surface structures
eLife 13:e96485.
https://doi.org/10.7554/eLife.96485
  1. Further reading

Further reading

    1. Structural Biology and Molecular Biophysics
    Colin H Peters, Rohit K Singh ... John R Bankston
    Research Article

    Lymphoid restricted membrane protein (LRMP) is a specific regulator of the hyperpolarization-activated cyclic nucleotide-sensitive isoform 4 (HCN4) channel. LRMP prevents cAMP-dependent potentiation of HCN4, but the interaction domains, mechanisms of action, and basis for isoform-specificity remain unknown. Here, we identify the domains of LRMP essential for this regulation, show that LRMP acts by disrupting the intramolecular signal transduction between cyclic nucleotide binding and gating, and demonstrate that multiple unique regions in HCN4 are required for LRMP isoform-specificity. Using patch clamp electrophysiology and Förster resonance energy transfer (FRET), we identified the initial 227 residues of LRMP and the N-terminus of HCN4 as necessary for LRMP to associate with HCN4. We found that the HCN4 N-terminus and HCN4-specific residues in the C-linker are necessary for regulation of HCN4 by LRMP. Finally, we demonstrated that LRMP-regulation can be conferred to HCN2 by addition of the HCN4 N-terminus along with mutation of five residues in the S5 region and C-linker to the cognate HCN4 residues. Taken together, these results suggest that LRMP inhibits HCN4 through an isoform-specific interaction involving the N-terminals of both proteins that prevents the transduction of cAMP binding into a change in channel gating, most likely via an HCN4-specific orientation of the N-terminus, C-linker, and S4-S5 linker.

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Isabelle Petit-Hartlein, Annelise Vermot ... Franck Fieschi
    Research Article

    NADPH oxidases (NOX) are transmembrane proteins, widely spread in eukaryotes and prokaryotes, that produce reactive oxygen species (ROS). Eukaryotes use the ROS products for innate immune defense and signaling in critical (patho)physiological processes. Despite the recent structures of human NOX isoforms, the activation of electron transfer remains incompletely understood. SpNOX, a homolog from Streptococcus pneumoniae, can serves as a robust model for exploring electron transfers in the NOX family thanks to its constitutive activity. Crystal structures of SpNOX full-length and dehydrogenase (DH) domain constructs are revealed here. The isolated DH domain acts as a flavin reductase, and both constructs use either NADPH or NADH as substrate. Our findings suggest that hydride transfer from NAD(P)H to FAD is the rate-limiting step in electron transfer. We identify significance of F397 in nicotinamide access to flavin isoalloxazine and confirm flavin binding contributions from both DH and Transmembrane (TM) domains. Comparison with related enzymes suggests that distal access to heme may influence the final electron acceptor, while the relative position of DH and TM does not necessarily correlate with activity, contrary to previous suggestions. It rather suggests requirement of an internal rearrangement, within the DH domain, to switch from a resting to an active state. Thus, SpNOX appears to be a good model of active NOX2, which allows us to propose an explanation for NOX2’s requirement for activation.