Characterization of cross-linking of cell walls of Bacillus subtilis by a combination of magic-angle spinning NMR and gas chromatography-mass spectrometry of both intact and hydrolyzed 13C- and 15N-labeled cell-wall peptidoglycan

In-cell NMR: Why and how?

NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.

Cells, drugs and NMR

Nuclear magnetic resonance (NMR) spectroscopy is a versatile tool for investigating cellular structures and their compositions. While in vivo and whole-cell NMR have a long tradition in cell-based approaches, high-resolution in-cell NMR spectroscopy is a new addition to these methods. In recent years, technological advancements in multiple areas provided converging benefits for cellular MR applications, especially in terms of robustness, reproducibility and physiological relevance. Here, we review the use of cellular NMR methods for drug discovery purposes in academia and industry. Specifically, we discuss how developments in NMR technologies such as miniaturized bioreactors and flow-probe perfusion systems have helped to consolidate NMR's role in cell-based drug discovery efforts.

Conformation of the phosphate D-alanine zwitterion in bacterial teichoic acid from nuclear magnetic resonance spectroscopy

The conformation of d-alanine (d-Ala) groups of bacterial teichoic acid is a central, yet untested, paradigm of microbiology. The d-Ala binds via the C-terminus, thereby allowing the amine to exist as a free cationic NH(3)(+) group with the ability to form a contact ion pair with the nearby anionic phosphate group. This conformation hinders metal chelation by the phosphate because the zwitterion pair is charge neutral. To the contrary, the repulsion of cationic antimicrobial peptides (CAMPs) is attributed to the presence of the d-Ala cation; thus the ion pair does not form in this model. Solid-state nuclear magnetic resonance (NMR) spectroscopy has been used to measure the distance between amine and phosphate groups within cell wall fragments of Bacillus subtilis. The bacteria were grown on media containing (15)N d-Ala and beta-chloroalanine racemase inhibitor. The rotational-echo double-resonance (REDOR) pulse sequence was used to measure the internuclear dipolar coupling, and the results demonstrate (1) the metal-free amine-to-phosphate distance is 4.4 A and (2) the amine-to-phosphate distance increases to 5.4 A in the presence of Mg(2+) ions. As a result, the zwitterion exists in a nitrogen-oxygen ion pair configuration providing teichoic acid with a positive charge to repel CAMPs. Additionally, the amine of d-Ala does not prevent magnesium chelation in contradiction to the prevailing view of teichoic acids in metal binding. Thus, the NMR-based description of teichoic acid structure resolves the contradictory models, advances the basic understanding of cell wall biochemistry, and provides possible insight into the creation of new antibiotic therapies.

XPS analysis of chemical functions at the surface of Bacillus subtilis

The surface chemical composition of nine strains of Bacillus subtilis was determined by X-ray photoelectron spectroscopy. Regressions between elemental concentrations and concentrations associated with different components of C1s, N1s, and O1s peaks provided a more precise validation of the procedure used for peak decomposition and allowed the assignment of the peak components to be completed or strengthened. The component of the O1s peak appearing around 531.2 eV was shown to contain a contribution of oxygen from phosphate groups (PO, PO-), the other contribution being due to oxygen involved in amide functions. The surface negative charge may be fully attributed to phosphate groups, despite the observation of two types of zeta potential vs pH curves. The strains exhibiting a sharp variation of the zeta potential (range of -35 to -55 mV) between pH 2 and 4.7 were characterized by a high phosphate surface concentration and by an excess (about 25%) of phosphate with respect to the sum of potassium, an exchangeable cation, and protonated nitrogen, attributed to protein or to alanine involved in teichoic acids.

Application of REDOR subtraction for filtered MAS observation of labeled backbone carbons of membrane-bound fusion peptides

Clean MAS observation of 13C-labeled carbons in membrane-bound HIV-1 and influenza fusion peptides was made by using a rotational-echo double-resonance spectroscopy (REDOR) filter of directly bonded 13C-15N pairs. The clean filtering achieved with the REDOR approach is superior to filtering done with sample difference spectroscopy. In one labeling approach, the peptide had labels at a single 13C carbonyl and its directly bonded 15N. The resulting chemical shift distribution of the filtered signal is used to assess the distribution of local secondary structures at the labeled carbonyl. For the influenza peptide, the Leu-2 carbonyl chemical shift distribution is shown to vary markedly with lipid and detergent composition, as well as peptide:lipid ratio, suggesting that the local peptide structure also has a strong dependence on these factors. Because most carboxylic- and amino-labeled amino acids are commercially available, this REDOR approach should have broad applicability to chemically synthesized peptides as well as bacterially synthesized proteins. In a second labeling approach, the HIV-1 fusion peptide had U-13C, 15N labeling over three sequential residues. When a 1.6 ms REDOR dephasing time is used, only backbone 13C signals are observed. The resulting spectra are used to determine spectral linewidths and to assess feasibility of assignment of uniformly labeled peptide.

Investigation of bacterial spore structure by high resolution solid-state nuclear magnetic resonance spectroscopy and transmission electron microscopy

High resolution solid-state nuclear magnetic resonance spectroscopy (NMR) in combination with transmission electron microscopy (TEM) of spores of Bacillus cereus, an outer coatless mutant B. subtilis 322, an inner coatless mutant B. subtilis 325 and of germinated spores of B. subtilis CMCC 604 were carried out. Structural differences in the coats, mainly protein of spores were reflected by NMR spectra which indicated also differences in molecular mobility of carbohydrates which was partially attributed to the cortex. Dipicolinic acid (DPA) of spores of B. cereus displayed a high degree of solid state order and may be crystalline. Heat activation was studied on spores of B. subtilis 357 lux + and revealed a structural change when analysed by TEM but this was not associated with increases in molecular mobility since no effects were measured by NMR.

Effects of hydration on molecular mobility in phase-bright Bacillus subtilis spores

The molecular mobility of 31P and 13C in dormant Bacillus subtilis spore samples with different water concentrations was investigated by high-resolution solid-state NMR. Lowest molecular mobility was observed in freeze-dried preparations. Rehydration to a 10% weight increase resulted in increases in molecular motions and addition of excess water furthered this effect. A spore slurry which had been freeze-dried displayed after addition of excess water similar NMR spectra to native wet preparations. Dipicolinic acid (DPA), which is mainly located in the core, was detected at all hydration levels in 13C cross-polarization magic angle spinning (CPMAS) but not in single-pulse magic angle spinning (SPMAS) spectra, indicating that hydration had no effect on its mobility. The molecular mobility of 31P, present mainly in core-specific components, was strongly dependent on hydration. This result suggests reversible water migration between inner spore compartments and the environment, whereas 13C spectra of DPA indicate that it is immobilized in a water-insoluble network in the core. Scanning transmission electron microscopy revealed that freeze-dried spores were significantly longer and narrower than fully hydrated spores and had a 3% smaller volume.

Spore peptidoglycan structure in a cwlD dacB double mutant of Bacillus subtilis

Bacillus subtilis cwlD and dacB mutants produce spore peptidoglycan (PG) with increased cross-linking but with little change in spore core hydration compared to the wild type. A cwlD dacB double mutant produced spores with a two- to fourfold greater increase in PG cross-linking and novel muropeptides containing glycine residues but no significant changes in spore resistance or core hydration.

Structure and dynamics of pentaglycyl bridges in the cell walls of Staphylococcus aureus by 13C-15N REDOR NMR

Whole cells and cell-wall fractions of Staphylococcusaureus have been labeled by various combinations of [1-13C]glycine, [15N]glycine, L--6-13C-lysine, L--6-15N-lysine, D--1-13C-alanine, and D--15N-alanine. The resulting materials have been examined using 13C and 15N solid-state, magic-angle spinning NMR techniques including cross-polarization, double cross-polarization, and rotational-echo double resonance. The results of these measurements indicate that the peptidoglycan glycyl bridges are complete (five units long) and form cross-links between three-quarters of all peptide stems. The pentaglycyl bridges are immobilized in lyophilized cell-wall fractions in a compact conformation with inter-residue spacings comparable to those of an alpha helix. The bridges have a similar compact conformation in intact whole cells, regardless of whether the cells have been lyophilized or were hydrated and frozen at -10 degrees C. The bridges are also in a time-averaged compact conformation in whole cells at 0 degrees C but with sizable structural fluctuations associated with local mobility. A small fraction of bridges are in extended-chain conformations.

Solid 13C CPMAS NMR spectroscopy studies of biosynthesis in whole cells of Methanosphaera stadtmanae

Whole cells of Methanosphaera stadtmanae were grown in media containing [13C]CO2, [2-13C]acetate, [1-13C]acetate, [3-13C]serine and [1-13C]formate. The label incorporation was determined using solid state 13C CPMAS NMR spectroscopy. The incorporation of serine hydroxymethyl carbon into the purine rings of nucleic acids and most probably the methyl group of thymine is demonstrated. The one carbon atom pathway shown in our previous work is operative in the biosynthesis of purines and pyrimidines. In addition, these studies clearly identified signals not observed in solution NMR spectroscopy and revealed an important pathway not previously known. The reversibility of formyl-containing one carbon atom carriers is demonstrated. The pattern of labeled carbon atoms in sugars confirms the biosynthetic route from pyruvate, which is formed from acetic acid and carbon dioxide. Finally, a preliminary lipid assignment is indicated. The solid state 13C CPMAS NMR of these intact cells proved to be a facile method to follow specific pathways.

Structural analysis of Bacillus subtilis 168 endospore peptidoglycan and its role during differentiation

The structure of the endospore cell wall peptidoglycan of Bacillus subtilis has been examined. Spore peptidoglycan was produced by the development of a method based on chemical permeabilization of the spore coats and enzymatic hydrolysis of the peptidoglycan. The resulting muropeptides which were >97% pure were analyzed by reverse-phase high-performance liquid chromatography, amino acid analysis, and mass spectrometry. This revealed that 49% of the muramic acid residues in the glycan backbone were present in the delta-lactam form which occurred predominantly every second muramic acid. The glycosidic bonds adjacent to the muramic acid delta-lactam residues were resistant to the action of muramidases. Of the muramic acid residues, 25.7 and 23.3% were substituted with a tetrapeptide and a single L-alanine, respectively. Only 2% of the muramic acids had tripeptide side chains and may constitute the primordial cell wall, the remainder of the peptidoglycan being spore cortex. The spore peptidoglycan is very loosely cross-linked at only 2.9% of the muramic acid residues, a figure approximately 11-fold less than that of the vegetative cell wall. The peptidoglycan from strain AA110 (dacB) had fivefold-greater cross-linking (14.4%) than the wild type and an altered ratio of muramic acid substituents having 37.0, 46.3, and 12.3% delta-lactam, tetrapeptide, and single L-alanine, respectively. This suggests a role for the DacB protein (penicillin-binding protein 5*) in cortex biosynthesis. The sporulation-specific putative peptidoglycan hydrolase CwlD plays a pivotal role in the establishment of the mature spore cortex structure since strain AA107 (cwlD) has spore peptidoglycan which is completely devoid of muramic acid delta-lactam residues. Despite this drastic change in peptidoglycan structure, the spores are still stable but are unable to germinate. The role of delta-lactam and other spore peptidoglycan structural features in the maintenance of dormancy, heat resistance, and germination is discussed.

31P-19F rotational-echo, double-resonance nuclear magnetic resonance experiment on fluoridated hydroxyapatite

This work demonstrates 31P-19F rotational-echo, double-resonance nuclear magnetic resonance (REDOR NMR), a simple experiment used to measure 31P-19F dipolar couplings. 19F-observed 31P-19F REDOR NMR of fluorapatite revealed the 31P-19F connectivities. 31P-observed 31P-19F REDOR NMR determined the nearest 31P-19F distance in fluorapatite. The application on fluoride-treated hydroxyapatite, the principal inorganic constituent of dental enamel and dentine, showed the formation of fluorohydroxyapatite with a surface coverage of less than one unit-cell layer.

The cortical peptidoglycan from spores of Bacillus megaterium and Bacillus subtilis is not highly cross-linked

Determination by amino acid analyses of the percentage of diaminopimelic acid in the spore cortex of Bacillus megaterium and Bacillus subtilis which is involved in interpeptide cross-links gave values of 31 to 37%. This finding supports the idea that the cortex volume could undergo significant changes in response to changes in pH or ionic strength and could thus play an active role in reducing the water content of the spore protoplast during sporulation.