Charting and unzipping the surface layer of Corynebacterium glutamicum with the atomic force microscope

Mapping the ultrastructural topology of the corynebacterial cell surface

Corynebacterium glutamicum is a diderm bacterium extensively used in the industrial-scale production of amino acids. Corynebacteria belong to the bacterial family Mycobacteriaceae, which is characterized by a highly unusual cell envelope with an outer membrane consisting of mycolic acids, called mycomembrane. The mycomembrane is further coated by a surface (S-)layer array in C. glutamicum, making this cell envelope highly distinctive. Despite the biotechnological significance of C. glutamicum and biomedical significance of mycomembrane-containing pathogens, ultrastructural and molecular details of its distinctive cell envelope remain poorly characterized. To address this, we investigated the cell envelope of C. glutamicum using electron cryotomography and cryomicroscopy of focused ion beam-milled single and dividing cells. Our cellular imaging allowed us to map the different components of the cell envelope onto the tomographic density. Our data reveal that C. glutamicum has a variable cell envelope, with the S-layer decorating the mycomembrane in a patchy manner. We further isolated and resolved the structure of the S-layer at 3.1 Å-resolution using single particle electron cryomicroscopy. Our structure shows that the S-layer of C. glutamicum is composed of a hexagonal array of the PS2 protein, which interacts directly with the mycomembrane via an anchoring segment containing a coiled-coil motif. Bioinformatic analyses revealed that the PS2 S-layer is sparsely yet exclusively present within the Corynebacterium genus and absent in other genera of the Mycobacteriaceae family, suggesting distinct evolutionary pathways in the development of their cell envelopes. Our structural and cellular data collectively provide a topography of the unusual C. glutamicum cell surface, features of which are shared by many pathogenic and microbiome-associated bacteria, as well as by several industrially significant bacterial species.

SymProFold: Structural prediction of symmetrical biological assemblies

Symmetry in nature often emerges from self-assembly processes and serves a wide range of functions. Cell surface layers (S-layers) form symmetrical lattices on many bacterial and archaeal cells, playing essential roles such as facilitating cell adhesion, evading the immune system, and protecting against environmental stress. However, the experimental structural characterization of these S-layers is challenging due to their self-assembly properties and high sequence variability. In this study, we introduce the SymProFold pipeline, which utilizes the high accuracy of AlphaFold-Multimer predictions to derive symmetrical assemblies from protein sequences, specifically focusing on two-dimensional S-layer arrays and spherical viral capsids. The pipeline tests all known symmetry operations observed in these systems (p1, p2, p3, p4, and p6) and identifies the most likely symmetry for the assembly. The predicted models were validated using available experimental data at the cellular level, and additional crystal structures were obtained to confirm the symmetry and interfaces of several SymProFold assemblies. Overall, the SymProFold pipeline enables the determination of symmetric protein assemblies linked to critical functions, thereby opening possibilities for exploring functionalities and designing targeted applications in diverse fields such as nanotechnology, biotechnology, medicine, and materials and environmental sciences.

Cryo-EM structure and polar assembly of the PS2 S-layer of Corynebacterium glutamicum

The polar-growing Corynebacteriales have a complex cell envelope architecture characterized by the presence of a specialized outer membrane composed of mycolic acids. In some Corynebacteriales, this mycomembrane is further supported by a proteinaceous surface layer or 'S-layer', whose function, structure and mode of assembly remain largely enigmatic. Here, we isolated ex vivo PS2 S-layers from the industrially important Corynebacterium glutamicum and determined its atomic structure by 3D cryoEM reconstruction. PS2 monomers consist of a six-helix bundle 'core', a three-helix bundle 'arm', and a C-terminal transmembrane (TM) helix. The PS2 core oligomerizes into hexameric units anchored in the mycomembrane by a channel-like coiled-coil of the TM helices. The PS2 arms mediate trimeric lattice contacts, crystallizing the hexameric units into an intricate semipermeable lattice. Using pulse-chase live cell imaging, we show that the PS2 lattice is incorporated at the poles, coincident with the actinobacterial elongasome. Finally, phylogenetic analysis shows a paraphyletic distribution and dispersed chromosomal location of PS2 in Corynebacteriales as a result of multiple recombination events and losses. These findings expand our understanding of S-layer biology and enable applications of membrane-supported self-assembling bioengineered materials.

The pH-responsive precipitation-redissolution of the CspB fusion protein, CspB50TEV-Teriparatide, triggered by changes in secondary structure

Cell surface protein B (CspB) fusion proteins can undergo reversible pH-responsive precipitation-redissolution. A pH-responsive precipitation-redissolution of CspB tag purification (pPRCP) method was established for protein purification using this property. However, the mechanism of the pH-responsive precipitation of CspB fusion proteins is unknown, which has made it difficult to set process parameters for pPRCP. In this study, we investigated the mechanism of the pH-responsive precipitation of CspB fusion proteins using CspB50TEV-Teriparatide (CspB-teri) as a model. As expected, CspB-Teri was reversibly precipitated at acidic pH. By contrast, CspB-Teri was not precipitated under unfolding conditions induced by trifluoroethanol, urea, or guanidine hydrochloride, even at acidic pH. The conformation of CspB-Teri changed to a β-sheet-rich structure as the pH decreased, followed by the formation of intermolecular interactions, which caused precipitation. The particle size of the CspB-Teri precipitate increased in a protein concentration-dependent manner. These results indicated that the pH-responsive precipitation of CspB-Teri is triggered by the formation of a β-sheet structure in response to decreasing pH, and the growth of the precipitate particles occurred through intermolecular interactions.

The Bacillus anthracis S-layer is an exoskeleton-like structure that imparts mechanical and osmotic stabilization to the cell wall

Surface layers (S-layers) are 2D paracrystalline protein monolayers covering the cell envelope of many prokaryotes and archaea. Proposed functions include a role in cell support, as scaffolding structure, as molecular sieve, or as virulence factor. Bacillus anthracis holds two S-layers, composed of Sap or EA1, which interchange in early and late exponential growth phase. We previously found that acute disruption of B. anthracis Sap S-layer integrity, by means of nanobodies, results in severe morphological cell surface defects and cell collapse. Remarkably, this loss of function is due to the destruction of the Sap lattice structure rather than detachment of monomers from the cell surface. Here, we combine force nanoscopy and light microscopy observations to probe the contribution of the S-layer to the mechanical, structural, and functional properties of the cell envelope, which have been so far elusive. Our experiments reveal that cells with a compromised S-layer lattice show a decreased compressive stiffness and elastic modulus. Furthermore, we find that S-layer integrity is required to resist cell turgor under hypotonic conditions. These results present compelling experimental evidence indicating that the S-layers can serve as prokaryotic exoskeletons that support the cell wall in conferring rigidity and mechanical stability to bacterial cells.

Solution design to extend the pH range of the pH-responsive precipitation of a CspB fusion protein

Cell surface protein B (CspB) from Corynebacterium glutamicum has been developed as a reversible pH-responsive tag for protein purification. CspB fusion proteins precipitate at acidic pH, after that they completely dissolve at neutral pH. This property has been used in a non-chromatographic protein purification method named pH-responsive Precipitation-Redissolution of CspB tag Purification (pPRCP). However, it is difficult to apply pPRCP to proteins that are unstable under acidic conditions. In an effort to shift the precipitation pH to a milder range, we investigated the solution conditions of CspB-fused Teriparatide (CspB50TEV-Teriparatide) during the process of pH-responsive precipitation using pPRCP. The purified CspB50TEV-Teriparatide in buffer without additives precipitated at pH 5.3. By contrast, CspB50TEV-Teriparatide in buffer with 0.5 M Na₂SO₄ precipitated at pH 6.6 because of the kosmotropic effect. Interestingly, the pH at which precipitation occurred was independent of the protein concentration. The precipitated CspB50TEV-Teriparatide was fully redissolved at above pH 8.0 in the presence or absence of salt. The discovery that proteins can be precipitated at a mild pH will allow pPRCP to be applied to acid-sensitive proteins.

Nutritional and functional values of lysed Corynebacterium glutamicum cell mass for intestinal health and growth of nursery pigs

The objective was to determine the nutritional and functional values of lysed Corynebacterium glutamicum cell mass (CGCM) as a protein supplement and a source of cell wall fragments supporting the growth and intestinal health of nursery pigs. Thirty-two pigs (21 d of age) were allotted to four treatments (n = 8) based on the randomized block design with sex and initial body weight (BW) as blocks. The main effect was the dietary supplementation of lysed CGCM (0, 0.7, 1.4, and 2.1%) replacing blood plasma and fed in two phases (10 and 11 d, respectively). Feed intake and BW were measured at the end of each phase. Pigs were euthanized on day 21 to collect jejunal tissue and mucosa to evaluate intestinal health. Ileal digesta were collected to measure the apparent ileal digestibility of nutrients in diets. Data were analyzed using Proc Mixed and Reg of SAS. Increasing daily intake of CGCM increased (linear; P < 0.05) ADG of pigs. Increasing CGCM supplementation affected (quadratic; P < 0.05) the relative abundance of Lactobacillaceae (minimum: 26.4% at 1.2% CGCM), Helicobacteraceae (maximum: 29.3% at 1.2% CGCM), and Campylobacteraceae (maximum: 9.0% at 1.0% CGCM). Increasing CGCM supplementation affected (quadratic; P < 0.05) the concentrations of immunoglobulin G (maximum: 4.94 µg/mg of protein at 1.0% CGCM) and protein carbonyl (PC; maximum: 6.12 nmol/mg of protein at 1.1% CGCM), whereas linearly decreased (P < 0.05) malondialdehyde (MDA) in the proximal jejunal mucosa. Increasing CGCM supplemention affected (quadratic; P < 0.05) intestinal enterocyte proliferation rate (maximum: 13.3% at 1.0% CGCM), whereas it did not affect intestinal morphology and the nutrient digestibility. In conclusion, supplementing 1.0% to 1.2%, reducing blood plasma supplementation by 0.7% to 0.9%, respectively, increased potential pathogenic microbiota associated in the jejunal mucosa resulting in increased immune response, enterocyte proliferation, and PC concentration. However, supplementing diets with 2.1% CGCM, replacing 1.5% blood plasma, improved growth performance, and reduced MDA without affecting nutrient digestibility, intestinal morphology, and microbiota in the jejunal mucosa. In this study, based on the polynomial contrast, supplementing 1.0% to 1.2% CGCM suppressed the benefits from blood plasma, whereas supplementing 2.1% CGCM showed functional benefits of CGCM with similar effects from blood plasma supplementation.

Lipid binding attenuates channel closure of the outer membrane protein OmpF

Outer-membrane porins are often considered as passive conduits of small molecules across lipid bilayers. Using native mass spectrometry experiments we identify a pH-sensitive lipid-binding mechanism of outer membrane porin F, which enables increased threading of a colicin-derived peptide through open channels. Supported by molecular dynamics simulations and channel recording experiments, we posit that this mechanism attenuates channel opening in response to changes in environmental conditions, specifically pH. These findings have important consequences for mass spectrometry experiments, wherein the role of charge is often overlooked, and they also could help provide understanding of antibiotics that gain access to Gram-negative bacteria through porin-mediated pathways.

Strong interactions between lipids and proteins occur primarily through association of charged headgroups and amino acid side chains, rendering the protonation status of both partners important. Here we use native mass spectrometry to explore lipid binding as a function of charge of the outer membrane porin F (OmpF). We find that binding of anionic phosphatidylglycerol (POPG) or zwitterionic phosphatidylcholine (POPC) to OmpF is sensitive to electrospray polarity while the effects of charge are less pronounced for other proteins in outer or mitochondrial membranes: the ferripyoverdine receptor (FpvA) or the voltage-dependent anion channel (VDAC). Only marginal charge-induced differences were observed for inner membrane proteins: the ammonia channel (AmtB) or the mechanosensitive channel. To understand these different sensitivities, we performed an extensive bioinformatics analysis of membrane protein structures and found that OmpF, and to a lesser extent FpvA and VDAC, have atypically high local densities of basic and acidic residues in their lipid headgroup-binding regions. Coarse-grained molecular dynamics simulations, in mixed lipid bilayers, further implicate changes in charge by demonstrating preferential binding of anionic POPG over zwitterionic POPC to protonated OmpF, an effect not observed to the same extent for AmtB. Moreover, electrophysiology and mass-spectrometry–based ligand-binding experiments, at low pH, show that POPG can maintain OmpF channels in open conformations for extended time periods. Since the outer membrane is composed almost entirely of anionic lipopolysaccharide, with similar headgroup properties to POPG, such anionic lipid binding could prevent closure of OmpF channels, thereby increasing access of antibiotics that use porin-mediated pathways.

A highly controllable protein self-assembly system with morphological versatility induced by reengineered host-guest interactions

Manipulating proteins to self-assemble into highly ordered nanostructures not only provides insights into the natural protein assembly process but also allows access to advanced biomaterials. Host-guest interactions have been widely used in the construction of artificial protein assemblies in recent years. CB[8] can selectively associate with two tripeptide Phe-Gly-Gly (FGG) tags with an extraordinarily high binding affinity (K_ter = 1.5 × 10¹¹ M^-2). However, the FGG tags utilized before are all fixed to the N-termini via genetic fusion; this spatial limitation greatly confined the availability of the CB[8]/FGG pair in the construction of more sophisticated protein nanostructures. Here we first designed and synthesized a maleimide-functionalized Phe-Gly-Gly tag as a versatile site-specific protein modification tool; this designed tag can site-selectively introduce desired guest moieties onto protein surfaces for host-guest driven protein assembly. When regulating the self-assembly process of proteins and CB[8], the constructed protein nanosystem can exhibit distinctive morphological diversities ranging from nanorings, nanospirals, nanowires to superwires. This work developed a new strategy for site-specific protein modification of the CB[8] binding tag and provides a possible direction for the construction of 'smart', dynamic self-assembly systems.

Introduction to Atomic Force Microscopy (AFM) in Biology

The atomic force microscope (AFM) has the unique capability of imaging biological samples with molecular resolution in buffer solution over a wide range of time scales from milliseconds to hours. In addition to providing topographical images of surfaces with nanometer- to angstrom-scale resolution, forces between single molecules and mechanical properties of biological samples can be investigated from the nano-scale to the micro-scale. Importantly, the measurements are made in buffer solutions, allowing biological samples to "stay alive" within a physiological-like environment while temporal changes in structure are measured-e.g., before and after addition of chemical reagents. These qualities distinguish AFM from conventional imaging techniques of comparable resolution, e.g., electron microscopy (EM). This unit provides an introduction to AFM on biological systems and describes specific examples of AFM on proteins, cells, and tissues. The physical principles of the technique and methodological aspects of its practical use and applications are also described. © 2016 by John Wiley & Sons, Inc.

Protein self-assembly via supramolecular strategies

Proteins, as the elemental basis of living organisms, mostly execute their biological tasks in the form of supramolecular self-assemblies with subtle architectures, dynamic interactions and versatile functionalities. Inspired by the structural harmony and functional beauty of natural protein self-assemblies to fabricate sophisticated yet highly ordered protein superstructures represents an adventure in the pursuit of nature's supreme wisdom. In this review, we focus on building protein self-assembly systems based on supramolecular strategies and classify recent progress by the types of utilized supramolecular driving forces. Especially, the design strategy, structure control and the thermodynamic/kinetic regulation of the self-assemblies, which will in turn provide insights into the natural biological self-assembly mechanism, are highlighted. In addition, recently, this research field is starting to extend its interest beyond constructing complex morphologies towards the potential applications of the self-assembly systems; several attempts to design functional protein complexes are also discussed. As such, we hope that this review will provide a panoramic sketch of the field and draw a roadmap towards the ultimate construction of advanced protein self-assemblies that even can serve as analogues of their natural counterparts.

A comparison of the surface nanostructure from two different types of gram-negative cells: Escherichia coli and Rhodobacter sphaeroides

Bacteria have been studied using different microscopy methods for many years. Recently, the developments of high-speed atomic force microscopy have opened the doors to study bacteria in new ways due to the fact that it uses much less force on the sample while imaging. This makes the high-speed atomic force microscope an indispensable technique for imaging the surface of living bacterial cells because it allows for the high-resolution visualization of surface proteins in their natural condition without disrupting the cell or the activity of the proteins. Previous work examining living cells of Magnetospirillum magneticum AMB-1 demonstrated that the surface of these bacteria was covered with a net-like structure that is mainly composed of porin molecules. However, it was unclear whether or not this feature was unique to other living bacteria. In this study we used the high-speed atomic force microscope to examine the surface of living cells of Escherichia coli and Rhodobacter sphaeroides to compare their structure with that of M. magneticum. Our research clearly demonstrated that both of these types of cells have an outer surface that is covered in a network of nanometer-sized holes similar to M. magneticum. The diameter of the holes was 8.0±1.5 nm for E. coli and 6.6±1.1 nm for R. sphaeroides. The results in this paper confirm that this type of outer surface structure exists in other types of bacteria and it is not unique to Magnetospirillum.

Microarrays and single molecules: an exciting combination

Biomolecules positioned at interfaces have spawned many applications in bioanalysis, biophysics, and cell biology. This Highlight describes recent developments in the research areas of protein and DNA arrays, and single-molecule sensing. We cover the ultrasensitive scanning of conventional microarrays as well as the generation of arrays composed of individual molecules. The combination of these tools has improved the detection limits and the dynamic range of microarray analysis, helped develop powerful single-molecule sequencing approaches, and offered biophysical examination with high throughput and molecular detail. The topic of this Highlight integrates several disciplines and is written for interested chemists, biophysicists and nanotechnologists.

Cell envelope of corynebacteria: structure and influence on pathogenicity

To date the genus Corynebacterium comprises 88 species. More than half of these are connected to human and animal infections, with the most prominent member of the pathogenic species being Corynebacterium diphtheriae, which is also the type species of the genus. Corynebacterium species are characterized by a complex cell wall architecture: the plasma membrane of these bacteria is followed by a peptidoglycan layer, which itself is covalently linked to a polymer of arabinogalactan. Bound to this, an outer layer of mycolic acids is found which is functionally equivalent to the outer membrane of Gram-negative bacteria. As final layer, free polysaccharides, glycolipids, and proteins are found. The composition of the different substructures of the corynebacterial cell envelope and their influence on pathogenicity are discussed in this paper.

Microbial cells analysis by atomic force microscopy

Unraveling the structure of microbial cells is a major challenge in current microbiology and offers exciting prospects in biomedicine. Atomic force microscopy (AFM) appears as a powerful method to image the surface ultrastructure of live cells under physiological conditions and allows real-time imaging to follow dynamic processes such as cell growth, and division and effects of drugs and chemicals. The following chapter introduces different methods of sample preparation to gain insights into the microbial cell organization. Successful strategies to immobilize microorganisms, including physical entrapment and chemical attachment, are described. This step is a key step and a prerequisite of any analysis and persists as an important limitation to the application of AFM to microbiology due to the wide diversity of microorganisms. Finally, some applications are depicted which underlie the ability of AFM to explore living microbes with unprecedented resolution.

Single-molecule force spectroscopy reveals the individual mechanical unfolding pathways of a surface layer protein

Surface layers (S-layers) represent an almost universal feature of archaeal cell envelopes and are probably the most abundant bacterial cell proteins. S-layers are monomolecular crystalline structures of single protein or glycoprotein monomers that completely cover the cell surface during all stages of the cell growth cycle, thereby performing their intrinsic function under a constant intra- and intermolecular mechanical stress. In gram-positive bacteria, the individual S-layer proteins are anchored by a specific binding mechanism to polysaccharides (secondary cell wall polymers) that are linked to the underlying peptidoglycan layer. In this work, atomic force microscopy-based single-molecule force spectroscopy and a polyprotein approach are used to study the individual mechanical unfolding pathways of an S-layer protein. We uncover complex unfolding pathways involving the consecutive unfolding of structural intermediates, where a mechanical stability of 87 pN is revealed. Different initial extensibilities allow the hypothesis that S-layer proteins adapt highly stable, mechanically resilient conformations that are not extensible under the presence of a pulling force. Interestingly, a change of the unfolding pathway is observed when individual S-layer proteins interact with secondary cell wall polymers, which is a direct signature of a conformational change induced by the ligand. Moreover, the mechanical stability increases up to 110 pN. This work demonstrates that single-molecule force spectroscopy offers a powerful tool to detect subtle changes in the structure of an individual protein upon binding of a ligand and constitutes the first conformational study of surface layer proteins at the single-molecule level.

Application of AFM from microbial cell to biofilm

Atomic Force Microscopy (AFM) has proven itself over recent years as an essential tool for the analysis of microbial systems. This article will review how AFM has been used to study microbial systems to provide unique insight into their behavior and relationship with their environment. Immobilization of live cells has enabled AFM imaging and force measurement to provide understanding of the structure and function of numerous microbial cells. At the macromolecular level AFM investigation into the properties of surface macromolecules and the energies associated with their mechanical conformation and functionality has helped unravel the complex interactions of microbial cells. At the level of the whole cell AFM has provided an integrated analysis of how the microbial cell exploits its environment through its selective, adaptable interface, the cell surface. In addition to these areas of study the AFM investigation of microbial biofilms has been vital for industrial and medical process analysis. There exists a tremendous potential for the future application of AFM to microbial systems and this has been strengthened by the trend to use AFM in combination with other characterization methods, such as confocal microscopy and Raman spectroscopy, to elucidate dynamic cellular processes.

Identifying assembly-inhibiting and assembly-tolerant sites in the SbsB S-layer protein from Geobacillus stearothermophilus

Surface layer (S-layer) proteins self-assemble into two-dimensional crystalline lattices that cover the cell wall of all archaea and many bacteria. We have generated assembly-negative protein variants of high solubility that will facilitate high-resolution structure determination. Assembly-negative versions of the S-layer protein SbsB from Geobacillus stearothermophilus PV72/p2 were obtained using an insertion mutagenesis screen. The haemagglutinin epitope tag was inserted at 23 amino acid positions known to be located on the monomer protein surface from a previous cysteine accessibility screen. Limited proteolysis, circular dichroism, and fluorescence were used to probe whether the epitope insertion affected the secondary and tertiary structures of the monomer, while electron microscopy and size-exclusion chromatography were employed to examine proteins' ability to self-assemble. The screen not only identified assembly-compromised mutants with native fold but also yielded correctly folded, self-assembling mutants suitable for displaying epitopes for biomedical and biophysical applications, as well as cryo-electron microscopy imaging. Our study marks an important step in the analysis of the S-layer structure. In addition, the approach of concerted insertion and cysteine mutagenesis can likely be applied for other supramolecular assemblies.

In vivo imaging of S-layer nanoarrays on Corynebacterium glutamicum

Crystalline bacterial cell surface layers (S-layers) are monomolecular arrays of (glyco)proteins that have recently produced a wealth of new opportunities in nanotechnology. Whereas the in vitro imaging of isolated S-layers is well established, their direct imaging on live cells remains very challenging. Here we use atomic force microscopy (AFM) to visualize S-layer nanoarrays on living Corynebacterium glutamicum bacteria. We demonstrate the presence of two highly ordered surface layers. The most external layer represents the hexagonal S-layer, and the inner layer displays regular patterns of nanogrooves that could act as a biomolecular template promoting the 2-D assembly of S-layer monomers. These nanoscale analyses open new avenues for understanding the structure of protein monomolecular arrays, which is a crucial challenge in current nanoscience and life science research.

Towards nanomicrobiology using atomic force microscopy

At the cross-roads of nanoscience and microbiology, the nanoscale analysis of microbial cells using atomic force microscopy (AFM) is an exciting, rapidly evolving research field. Over the past decade, there has been tremendous progress in our use of AFM to observe membrane proteins and live cells at high resolution. Remarkable advances have also been made in applying force spectroscopy to manipulate single membrane proteins, to map surface properties and receptor sites on cells and to measure cellular interactions at the single-cell and single-molecule levels. In addition, recent developments in cantilever nanosensors have opened up new avenues for the label-free detection of microorganisms and bioanalytes.

Atomic force microscopy of biological membranes

Atomic force microscopy (AFM) is an ideal method to study the surface topography of biological membranes. It allows membranes that are adsorbed to flat solid supports to be raster-scanned in physiological solutions with an atomically sharp tip. Therefore, AFM is capable of observing biological molecular machines at work. In addition, the tip can be tethered to the end of a single membrane protein, and forces acting on the tip upon its retraction indicate barriers that occur during the process of protein unfolding. Here we discuss the fundamental limitations of AFM determined by the properties of cantilevers, present aspects of sample preparation, and review results achieved on reconstituted and native biological membranes.

Introduction to atomic force microscopy (AFM) in biology

The atomic force microscope has the unique capability of imaging biological samples with molecular resolution in buffer solution. In addition to providing topographical images of surfaces with nanometer- to angstrom-scale resolution, forces between single molecules and mechanical properties of biological samples can be investigated. Importantly, the measurements are made in buffer solutions, allowing biological samples to stay alive within a physiological-like environment while temporal changes in structure are measured. This overview provides an introduction to AFM on biological systems and describes specific examples of AFM on proteins. The physical principles of the technique and methodological aspects of its practical use and applications are also described.

The surface location of individual residues in a bacterial S-layer protein

Bacterial surface layer (S-layer) proteins self-assemble into large two-dimensional crystalline lattices that form the outermost cell-wall component of all archaea and many eubacteria. Despite being a large class of self-assembling proteins, little is known about their molecular architecture. We investigated the S-layer protein SbsB from Geobacillus stearothermophilus PV72/p2 to identify residues located at the subunit-subunit interface and to determine the S-layer's topology. Twenty-three single cysteine mutants, which were previously mapped to the surface of the SbsB monomer, were subjected to a cross-linking screen using the photoactivatable, sulfhydryl-reactive reagent N-[4-(p-azidosalicylamido)butyl]-3'-(2'-pyridyldithio)propionamide. Gel electrophoretic analysis on the formation of cross-linked dimers indicated that 8 out of the 23 residues were located at the interface. In combination with surface accessibility data for the assembled protein, 10 residues were assigned to positions at the inner, cell-wall-facing lattice surface, while 5 residues were mapped to the outer, ambient-exposed lattice surface. In addition, the cross-linking screen identified six positions of intramolecular cross-linking within the assembled protein but not in the monomeric S-layer protein. Most likely, these intramolecular cross-links result from conformational changes upon self-assembly. The results are an important step toward the further structural elucidation of the S-layer protein via, for example, X-ray crystallography and cryo-electron microscopy. Our approach of identifying the surface location of residues is relevant to other planar supramolecular protein assemblies.

Exploring the molecular forces within and between CbsA S-layer proteins using single molecule force spectroscopy

We used single molecule atomic force microscopy (AFM) to gain insight into the molecular forces driving the folding and assembly of the S-layer protein CbsA. Force curves recorded between tips and supports modified with CbsA proteins showed sawtooth patterns with multiple force peaks of 58+/-26pN that we attribute to the unfolding of alpha-helices, in agreement with earlier secondary structure predictions. The average unfolding force increased with the pulling speed but was independent on the interaction time. Force curves obtained for CbsA peptides truncated in their C-terminal region showed similar periodic features, except that fewer force peaks were seen. Furthermore, the average unfolding force was 83+/-45pN, suggesting the domains were more stable. By contrast, cationic peptides truncated in their N-terminal region showed single force peaks of 366+/-149pN, presumably reflecting intermolecular electrostatic bridges rather than unfolding events. Interestingly, these large intermolecular forces increased not only with pulling speed but also with interaction time. We expect that the intra- and intermolecular forces measured here may play a significant role in controlling the stability and assembly of the CbsA protein.

Two-chamber AFM: probing membrane proteins separating two aqueous compartments

Biological membranes compartmentalize and define physical borders of cells. They are crowded with membrane proteins that fulfill diverse crucial functions. About one-third of all genes in organisms code for, and the majority of drugs target, membrane proteins. To combine structure and function analysis of membrane proteins, we designed a two-chamber atomic force microscopy (AFM) setup that allows investigation of membranes spanned over nanowells, therefore separating two aqueous chambers. We imaged nonsupported surface layers (S layers) of Corynebacterium glutamicum at sufficient resolution to delineate a 15 A-wide protein pore. We probed the elastic and yield moduli of nonsupported membranes, giving access to the lateral interaction energy between proteins. We combined AFM and fluorescence microscopy to demonstrate the functionality of proteins in the setup by documenting proton pumping by Halobacterium salinarium purple membranes.

The surface (S)-layer gene cspB of Corynebacterium glutamicum is transcriptionally activated by a LuxR-type regulator and located on a 6 kb genomic island absent from the type strain ATCC 13032

The surface (S)-layer gene region of the Gram-positive bacterium Corynebacterium glutamicum ATCC 14067 was identified on fosmid clones, sequenced and compared with the genome sequence of C. glutamicum ATCC 13032, whose cell surface is devoid of an ordered S-layer lattice. A 5·97 kb DNA region that is absent from the C. glutamicum ATCC 13032 chromosome was identified. This region includes cspB, the structural gene encoding the S-layer protomer PS2, and six additional coding sequences. PCR experiments demonstrated that the respective DNA region is conserved in different C. glutamicum wild-type strains capable of S-layer formation. The DNA region is flanked by a 7 bp direct repeat, suggesting that illegitimate recombination might be responsible for gene loss in C. glutamicum ATCC 13032. Transfer of the cloned cspB gene restored the PS2− phenotype of C. glutamicum ATCC 13032, as confirmed by visualization of the PS2 proteins by SDS-PAGE and imaging of ordered hexagonal S-layer lattices on living C. glutamicum cells by atomic force microscopy. Furthermore, the promoter of the cspB gene was mapped by 5′ rapid amplification of cDNA ends PCR and the corresponding DNA fragment was used in DNA affinity purification assays. A 30 kDa protein specifically binding to the promoter region of the cspB gene was purified. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry and peptide mass fingerprinting of the purified protein led to the identification of the putative transcriptional regulator Cg2831, belonging to the LuxR regulatory protein family. Disruption of the cg2831 gene in C. glutamicum resulted in an almost complete loss of PS2 synthesis. These results suggested that Cg2831 is a transcriptional activator of cspB gene expression in C. glutamicum.

Watching the components of photosynthetic bacterial membranes and their in situ organisation by atomic force microscopy

The atomic force microscope has developed into a powerful tool in structural biology allowing information to be acquired at submolecular resolution on the protruding structures of membrane proteins. It is now a complementary technique to X-ray crystallography and electron microscopy for structure determination of individual membrane proteins after extraction, purification and reconstitution into lipid bilayers. Moving on from the structures of individual components of biological membranes, atomic force microscopy has recently been demonstrated to be a unique tool to identify in situ the individual components of multi-protein assemblies and to study the supramolecular architecture of these components allowing the efficient performance of a complex biological function. Here, recent atomic force microscopy studies of native membranes of different photosynthetic bacteria with different polypeptide contents are reviewed. Technology, advantages, feasibilities, restrictions and limits of atomic force microscopy for the acquisition of highly resolved images of up to 10 A lateral resolution under native conditions are discussed. From a biological point of view, the new insights contributed by the images are analysed and discussed in the context of the strongly debated organisation of the interconnected network of membrane-associated chlorophyll-protein complexes composing the photosynthetic apparatus in different species of purple bacteria.

Probing bacterial interactions: integrated approaches combining atomic force microscopy, electron microscopy and biophysical techniques

Recent developments in the application of Atomic Force Microscopy (AFM) and other biophysical techniques for the study of bacterial interactions and adhesion are discussed in the light of established biological and microscopic approaches. Whereas molecular-biological techniques combined with electron microscopy allow the identification and localization of surface constituents mediating bacterial interactions, with AFM it has become possible to actually measure the forces involved in bacterial interactions. Combined with the flexibility of AFM in probing various types of physical interactions, such as electrostatic interactions, specific ligand-receptor interactions and the elastic forces of deformation and extension of bacterial surface polymers and cell wall, this provides prospects for the elucidation of the biophysical mechanism of bacterial interaction. However, because of the biochemical and a biophysical complexity of the bacterial cell wall, integrated approaches combining AFM with electron microscopy and biophysical techniques are needed to elucidate the mechanism by which a bacterium interacts with a host or material surface. The literature on electron microscopy of the bacterial cell wall is reviewed, with particular emphasis on the staining of specific classes of cell-wall constituents. The application of AFM in the analysis of bacterial surfaces is discussed, including AFM operating modes, sample preparation methods and results obtained on various strains. For various bacterial strains, the integration of EM and AFM data is discussed. Various biophysical aspects of the analysis of bacterial surface structure and interactions are discussed, including the theory of colloidal interactions and Bell's theory of cell-to-cell adhesion. An overview is given of biophysical techniques used in the analysis of the properties of bacterial surfaces and bacterial surface constituents and their integration with AFM. Finally, we discuss recent progress in the understanding of the role of bacterial interactions in medicine within the framework of the techniques and concepts discussed in the paper.

Classification of hyper-variable Corynebacterium glutamicum surface-layer proteins by sequence analyses and atomic force microscopy

The structural S-layer proteins of 28 different Corynebacterium glutamicum isolates have been analyzed systematically. Treatment of whole C. glutamicum cells with detergents resulted in the isolation of S-layer proteins with different apparent molecular masses, ranging in size from 55 to 66 kDa. The S-layer genes analyzed were characterized by coding regions ranging from 1,473 to 1,533 nucleotides coding for S-layer proteins with a size of 490-510 amino acids. Using PCR techniques, the corresponding S-layer genes of the 28 C. glutamicum isolates were all cloned and sequenced. The deduced amino acid sequences of the S-layer proteins showed identities between 69 and 98% and could be grouped into five phylogenetic classes. Furthermore, sequence analyses indicated that the S-layer proteins of the analyzed C. glutamicum isolates exhibit a mosaic structure of highly conserved and highly variable regions. Several conserved regions were assumed to play a key role in the formation of the C. glutamicum S-layers. Especially the N-terminal signal peptides and the C-terminal anchor sequences of the S-layer proteins showed a nearly perfect amino acid sequence conservation. Analyses by atomic force microscopy revealed a committed hexagonal structure. Morphological diversity of the C. glutamicum S-layers was observed in a class-specific unit cell dimension (ranging from 15.2 to 17.4 nm), which correlates with the sequence similarity-based classification. It could be demonstrated that differences in the primary structure of the S-layer proteins were reflected by the S-layer morphology.

The cell wall of lactic acid bacteria: surface constituents and macromolecular conformations

A variety of strains of the genus Lactobacillus was investigated with respect to the structure, softness, and interactions of their outer surface layers in order to construct structure-property relations of the Gram-positive bacterial cell wall. The role of the conformational properties of the constituents of the outer cell-wall layers and their spatial distribution on the cell wall is emphasized. Atomic force microscopy was used to resolve the surface structure, interactions, and softness of the bacterial cell wall at nanometer-length scales and upwards. The pH-dependence of the electrophoretic mobility and a novel interfacial adhesion assay were used to analyze the average physicochemical properties of the bacterial strains. The bacterial surface is smooth when a compact layer of globular proteins constitutes the outer surface, e.g., the S-layer of L. crispatus DSM20584. In contrast, for two other S-layer containing strains (L. helveticus ATCC12046 and L. helveticus ATCC15009), the S-layer is covered by polymeric surface constituents which adopt a much more extended conformation and which confer a certain roughness to the surface. Consequently, the S-layer is important for the overall surface properties of L. crispatus, but not for the surface properties of L. helveticus. Both surface proteins (L. crispatus DSM20584) and (lipo)teichoic acids (L. johnsonii ATCC332) confer hydrophobic properties to the bacterial surface whereas polysaccharides (L. johnsonii DSM20533 and L. johnsonii ATCC 33200) render the bacterial surface hydrophilic. Using the interfacial adhesion assay, it was demonstrated that hydrophobic groups within the cell wall adsorb limited quantities of hydrophobic compounds. The present work demonstrates that the impressive variation in surface properties displayed by even a limited number of genetically-related bacterial strains can be understood in terms of established colloidal concepts, provided that sufficiently detailed structural, chemical, and conformational information on the surface constituents is available.

Imaging of lactic acid bacteria with AFM--elasticity and adhesion maps and their relationship to biological and structural data

The adhesion of lactic acid bacteria to the intestinal epithelium is one of the most important factors determining probiotic ability of a bacterial strain. Studying bacterial adhesion requires knowledge of the structure and properties of the bacterial surface, which can be studied by atomic force microscopy under native conditions. The observation of the surface topography of bacteria from the species Lactobacillus crispatus, L. helveticus and L. johnsonii shows major differences between bacteria having a crystalline-like protein layer as part of the cell wall and those without such layers. Force volume images calculated into elasticity and adhesion force maps of different bacterial strains show that L. crispatus and L. helveticus have a surface with a homogeneous stiffness with no adhesion events. This is most likely caused by the S-layer, which completely covers the surface of the bacteria. We infer that the absence of adhesion peaks is caused by the semi-crystalline character of such protein layers, in agreement with the results obtained from electron microscopy. Analysis of a number of L. johnsonii strains shows that these bacteria have surface properties which strongly differ from the L. crispatus and L. helveticus strains. For L. johnsonii DMS20533 and L. johnsonii ATCC33200 high adhesion forces are observed, which can be related to a surface rich in polysaccharides. L. johnsonii ATCC332 has lower adhesion forces compared to the other two and, furthermore, the surface topography shows depressions. We suppose that this strain has a surface pattern consisting of crystalline-like proteins alternating with polysaccharide-rich domains. The wide variety in surface properties of lactobacilli could well have wide-ranging implications for food processing and for health benefits.

Mycomembrane and S-layer: two important structures of Corynebacterium glutamicum cell envelope with promising biotechnology applications

Corynebacteria belong to a distinct Gram-positive group of bacteria including mycobacteria and nocardia, which are characterized by the presence of mycolic acids in their cell wall. These bacteria share the property of having an unusual cell envelope structural organization close to Gram-negative bacteria. In addition to the inner membrane, the cell envelope is constituted of a thick arabinogalactan-peptidoglycan polymer covalently linked to an outer lipid layer, which is mainly composed of mycolic acids and probably organized in an outer membrane like structure. In some species, the cell is covered by a crystalline surface layer composed of a single protein species, which is anchored in the outer membrane like barrier. An increasing number of reports have led to a better understanding of the structure of the cell wall of Corynebacterium glutamicum. These works included the characterization of several cell wall proteins like S-layer protein and porins, genetic and biochemical characterization of mycolic acids biosynthesis, ultrastructural description of the cell envelope, and chemical analysis of its constituents. All these data address new aspects regarding cell wall permeability towards macromolecules and amino acids but also open new opportunities for biotechnology applications.

Direct real-time molecular scale visualisation of the degradation of condensed DNA complexes exposed to DNase I

The need to protect DNA from in vivo degradation is one of the basic tenets of therapeutic gene delivery and a standard test for any proposed delivery vector. The currently employed in vitro tests, however, presently provide no direct link between the molecular structure of the vector complexes and their success in this role, thus hindering the rational design of successful gene delivery agents. Here we apply atomic force microscopy (AFM) in liquid to visualise at the molecular scale and in real time, the effect of DNase I on generation 4 polyamidoamine dendrimers (G4) complexed with DNA. These complexes are revealed to be dynamic in nature showing a degree of mobility, in some cases revealing the addition and loss of dendrimers to individual complexes. The formation of the G4-DNA complexes is observed to provide a degree of protection to the DNA. This protection is related to the structural morphology of the formed complex, which is itself shown to be dependent on the dendrimer loading and the time allowed for complex formation.

Recent progress in the application of atomic force microscopy imaging and force spectroscopy to microbiology

Atomic force microscopy imaging and force spectroscopy have recently opened a range of novel applications in microbiology. During the past two years, rapid advances have been made using atomic force microscopy to visualize the surface structure of two-dimensional bacterial protein crystals, biofilms and individual cells in physiological conditions. There has also been remarkable progress in using force spectroscopy to measure biomolecular interactions and physical properties of microbial surfaces. Specific highlights include the imaging and manipulation of membrane proteins at the subnanometer level, the observation of the surface of living cells at high resolution, the mapping of local properties such as surface charges, the measurement of elastic properties of cell-surface constituents and the probing of cellular interactions using functionalized probes.

Progress in the analysis of membrane protein structure and function

Structural information on membrane proteins is sparse, yet they represent an important class of proteins that is encoded by about 30% of all genes. Progress has primarily been achieved with bacterial proteins, but efforts to solve the structure of eukaryotic membrane proteins are also increasing. Most of the structures currently available have been obtained by exploiting the power of X-ray crystallography. Recent results, however, have demonstrated the accuracy of electron crystallography and the imaging power of the atomic force microscope. These instruments allow membrane proteins to be studied while embedded in the bi-layer, and thus in a functional state. The low signal-to-noise ratio of cryo-electron microscopy is overcome by crystallizing membrane proteins in a two-dimensional protein-lipid membrane, allowing its atomic structure to be determined. In contrast, the high signal-to-noise ratio of atomic force microscopy allows individual protein surfaces to be imaged at sub-nanometer resolution, and their conformational states to be sampled. This review summarizes the steps in membrane protein structure determination and illuminates recent progress.