Isolation and characterization of the lipid A domain of lipopolysaccharide (LPS) from gram-negative bacteria provides insight into cell surface based mechanisms of antibiotic resistance, bacterial survival and fitness, and how chemically diverse lipid A molecular species differentially modulate host innate immune responses.
Lipopolysaccharide (LPS) is the major cell surface molecule of gram-negative bacteria, deposited on the outer leaflet of the outer membrane bilayer. LPS can be subdivided into three domains: the distal O-polysaccharide, a core oligosaccharide, and the lipid A domain consisting of a lipid A molecular species and 3-deoxy-D-manno-oct-2-ulosonic acid residues (Kdo). The lipid A domain is the only component essential for bacterial cell survival. Following its synthesis, lipid A is chemically modified in response to environmental stresses such as pH or temperature, to promote resistance to antibiotic compounds, and to evade recognition by mediators of the host innate immune response. The following protocol details the small- and large-scale isolation of lipid A from gram-negative bacteria. Isolated material is then chemically characterized by thin layer chromatography (TLC) or mass-spectrometry (MS). In addition to matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) MS, we also describe tandem MS protocols for analyzing lipid A molecular species using electrospray ionization (ESI) coupled to collision induced dissociation (CID) and newly employed ultraviolet photodissociation (UVPD) methods. Our MS protocols allow for unequivocal determination of chemical structure, paramount to characterization of lipid A molecules that contain unique or novel chemical modifications. We also describe the radioisotopic labeling, and subsequent isolation, of lipid A from bacterial cells for analysis by TLC. Relative to MS-based protocols, TLC provides a more economical and rapid characterization method, but cannot be used to unambiguously assign lipid A chemical structures without the use of standards of known chemical structure. Over the last two decades isolation and characterization of lipid A has led to numerous exciting discoveries that have improved our understanding of the physiology of gram-negative bacteria, mechanisms of antibiotic resistance, the human innate immune response, and have provided many new targets in the development of antibacterial compounds.
Lipopolysaccharide (LPS) is the major outer surface molecule of nearly all gram-negative organisms and consists of three molecular domains: a distal O-antigen polysaccharide, a core oligosaccharide, and the membrane-associated lipid A domain deposited on the outer leaflet of the outer membrane bilayer1,2. The lipid A domain consists of 3-deoxy-D-manno-oct-2-ulosonic (Kdo) residues and a lipid A molecular species, where lipid A can be defined as the chloroform soluble portion of LPS upon mild-acid hydrolysis1,2. The standard lipid A molecule can be chemically defined as a diglucosamine backbone that is hexa-acylated and bis-phosphorylated; consistent with the major lipid A species observed in the model organism Escherichia coli (E. coli)1,2. Nine constitutively expressed genes, conserved throughout gram-negative bacteria, are responsible for the production of the lipid A domain (Figure 1)1,2. Most bacteria have an additional set of genes, which vary in degree of phylogenetic conservation, that participate in further chemical modification of lipid A3. Dephosphorylation, removal of acyl chains, and the addition of chemical moieties such as amino sugars (e.g. aminoarabinose) and/or phosphoethanolamine are the most commonly observed activities (Figure 1). Many of the enzymes responsible for lipid A modification are directly activated by environmental signals, such as divalent cations, or their expression is regulated by two component response-regulator systems3.
Recognition of lipid A species by the host innate immune system is mediated by the Toll-like receptor 4/myeloid differentiation factor 2 (TLR4/MD2) co-receptor4. Hydrophobic forces between MD2 and the lipid A acyl chains, as well as between TLR4 and the 1 and 4 ‘phosphate groups of lipid A promote the strong association of lipid A with TLR4/MD24,5. Modifications that alter acylation state or the negative charge of lipid A impact TLR4/MD2 based lipid A recognition and downstream stimulation of the innate immune response activators NF-κB and mediators of inflammation such as TNFα and IL1-β6,7. Modifications that mask the negative charge of lipid A also prevent bactericidal cationic antimicrobial peptides from binding to gram-negative cell surfaces3,8. Many lipid A modifications are hypothesized to increase bacterial fitness under specific environmental conditions, such as inside the human host or in an ecological niche. For this reason many modification enzymes are attractive targets in the rational development of antimicrobial compounds. The chemical diversity of lipid A structures, with respect to organism and/or environment, and the biological implications of these diverse structures make the structural characterization of lipid A an important endeavor in the study of gram-negative bacteria.
Isolation of lipid A molecules from whole bacteria involves the extraction of LPS from the bacterial cell surface, a hydrolytic step to liberate lipid A, followed by a final purification procedure9-11. The most frequently cited LPS extraction procedure is the hot-phenol water extraction procedure, first introduced by Westphal and Jann10. After extraction whole LPS is subjected to mild-acid hydrolysis, which chemically separates Kdo from the 6′-hydroxyl of the distal glucosamine sugar of lipid A (Figure 1). Numerous pitfalls exist for the hot-phenol water procedure including the use of a high hazard reagent, the need to degrade co-extracted nucleic acids and proteins, and several days are required to complete the protocol10.
Our lab has further developed the extraction and isolation of lipid A as first developed by Caroff and Raetz12,13. Compared to hot-phenol water procedures, the method presented here is more rapid and efficient and accommodates a wide range of culture volumes from 5 ml to multiple liters. Moreover, unlike hot-phenol water extractions, our method does not select for rough- or smooth-types of LPS, providing optimal recovery of lipid A species. In our protocol, chemical lysis of whole bacterial cells is performed using a mixture of chloroform, methanol and water, where LPS can be pelleted by centrifugation. A combination of mild-acid hydrolysis and solvent extractions (Bligh-Dyer) are used to liberate lipid A from covalently attached polysaccharide. The method of Bligh and Dyer was first applied to the extraction of lipid species from a variety of animal and plant tissues14, modified here to separate hydrolyzed polysaccharide from lipid A. In this final separation step, chloroform soluble lipids selectively partition into the lower organic phase. To further purify lipid A, reverse-phase or anionic exchange column chromatography can be used12.
After isolation of lipid A species from whole cells, a number of analytical methods can be used to characterize the chemical structure of the isolated material such as NMR, TLC, and MS-based analysis. NMR allows for non-destructive structural elucidation, and provides structural detail related to glycosidic linkages, unequivocal assignment of acyl chain positions, and assignment of attachment sites for lipid A modifications like aminoarabinose or phosphoethanolamine15-17. NMR analysis of lipid A is not discussed within our protocol, but has been described adequately elsewhere15,16. For rapid analysis TLC based methods are frequently used, but fail to provide direct information regarding fine chemical structure. MS based protocols are the most frequently employed method to characterize lipid A structures18,19. Matrix associated laser desorption ionization (MALDI)-MS is often used to initially survey intact lipid A species. Singly charged ions are generated from analyte prepared according to our extraction procedures. As more fine structural analysis is required, MS/MS based methods prove more informative than MALDI-MS. Coupled to electrospray ionization (ESI) singly or multiply charged lipid A precursor ions are further fragmented by collision induced dissociation (CID) or ultraviolet photodissociation (UVPD), to generate structurally informative product ions18,20,21. Neutral loss products from lipid A precursor ions are also frequently generated during ESI-MS providing an additional layer of structural information.
Tandem mass spectrometry (MS/MS) has proven to be an indispensable and versatile method for the elucidation of lipid A structures. During MS/MS, ions are activated to yield a diagnostic fragmentation pattern that can be used to elucidate the structure of the precursor ion. The most widely available MS/MS method is CID. This method produces fragment ions via collisions of the selected precursor ion with an inert target gas, resulting in energy deposition that leads to dissociation. CID has proven a critical tool in the assignment of lipid A structure for a wide range of bacterial species22-33.
Although CID is the most universally implemented MS/MS method, it generates a limited array of product ions. 193 nm UVPD is an alternative and complementary MS/MS method. This method uses a laser to irradiate ions, and the absorption of photons results in energization of the ions and subsequent dissociation. This higher energy MS/MS technique produces a more diverse array of product ions than CID and thus provides more informative fragmentation patterns. In particular, UVPD affords information about subtle changes in lipid A species based on cleavages at glycosidic, amine, acyl and C-C linked bonds18,21,34.
All solutions should be prepared with ultrapure water and HPLC grade methanol and chloroform. Prepared solutions that contain organic solvents such as methanol, chloroform, or pyridine and concentrated acids or bases should be prepared and used under a chemical fume hood. All solutions can be stored at RT. Solvents should be measured in a graduated glass cylinder and stored in glass solvent bottles with PTFE lined caps. For long-term storage chloroform-containing solvents should be stored in tinted amber glass bottles to avoid the production of phosgene, a highly reactive acid chloride. PTFE centrifuge tubes and rotary evaporator flasks should be rinsed with methanol and chloroform before use. Follow necessary federal, state and/or institutional waste disposal regulations when disposing of solvents and/or radioactive waste.
1. Large Scale Lipid A Extraction (50 ml to 1.5 L)
2. Visualization of Lipid A Species via Thin Layer Chromatography
3. Structural Characterization of Lipid A via MALDI-TOF Mass Spectrometry
4. Electrospray Ionization Mass Spectrometry and Collision Induced Dissociation of Lipid A
5. MS/MS on Lipid A by Ultraviolet Photodissociation
6. 32P-Labeling of Lipid A and Subsequent Isolation
7. Visualization of 32P-labeled Lipid A Species via Thin Layer Chromatography
Canonical lipid A of E. coli and Salmonella enterica serovar Typhimurium is a hexa-acylated disaccharide of glucosamine with phosphate groups at the 1- and 4 ‘-positions. During growth in rich media (e.g. Luria Broth) a portion of the lipid A contains a pyrophosphate group at the 1-position yielding a tris-phosphorylated species36 (Figure 1). Kdo (3-deoxy-D-manno-octulosonic acid), is attached at the 6′-hydroxyl and serves as a bridge to link lipid A to the remaining carbohydrate domains (i.e. core oligosaccharide and O-antigen domains) of LPS. Although gram-negative bacteria share a conserved pathway for lipid A biosynthesis similar to that of E. coli K-12, there is a large amount of diversity in lipid A structures. This diversity arises from the action of latent enzymes that modify the lipid A structure, which are activated in response to environmental stimuli. For example, in S. enterica the phosphate groups of lipid A can be modified with the cationic sugar L-4-aminoarabinose (Figure 1; blue) or with a phosphoethanolamine residue (Figure 1; magenta). In Salmonella these modifications are regulated by two-component response regulator systems, added in response to low [Mg2+], mild-acidic pH, and the presence of cationic antimicrobial peptides. Additionally in Salmonella, palmitate can be added to form a hepta-acylated lipid A, which promotes resistance to cationic antimicrobial peptides (Figure 1; green)8. Other modifications include, but are not limited to, removal of phosphate groups and acyl chains, or dioxygenase catalyzed addition of a hydroxyl group to the 3′-linked secondary acyl chain observed in a number of organisms1,3.
Isolation of intact lipid A from whole cells by our modification of the method of Caroff and Raetz is described in protocol 1 (Figure 2). This isolation method has been used to estimate that 106 molecules of lipid A exist per bacterial cell of E. coli37. Following protocols 1 and 3, the negative ion MALDI-TOF mass spectrum of lipid A from E. coli K-12 (W3110) yields the singly deprotonated ion ([M-H]–) at m/z 1,796.20 as the majorly observed species (Figure 3). MALDI-TOF MS was performed in negative-reflectron mode to improve spectral resolution. Alternatively, the same lipid sample subjected to negative mode nano-ESI (Protocol 4) yields predominately doubly deprotonated lipid A ions at m/z 898.1 denoted by [M-2H]2- (Figure 4). Singly deprotonated lipid A ions [M-H]– at m/z 1,796.20 are observable, but are of lower relative abundance to [M-2H]2- ions (Figure 4). Multiply charged species predominate when using ESI. Fragmentation by CID (Figure 5A) or 193 nm UVPD (Figure 5B) was performed on the [M-H]– lipid A ion m/z 1,796.20. These techniques can be used to better assign chemical structures, particularly of lipid A species containing complex combinations of modifications, or previously uncharacterized chemical modifications. Fragmentation profiles are shown with dashed lines representing cleavage sites and are matched with the m/z values below each provided structure (Figure 5). The m/z values and cleavage sites highlighted in red font represent unique product ions associated with UVPD.
As described in protocols 6 and 7, 32P-labeled lipid A isolated from two different E. coli K-12 strains was analyzed by TLC (Figure 6). W3110 contains mostly bis- and tris- phosphorylated lipid A (Figure 6; left lane), whereas a more complex TLC pattern is observed with 32P-lipid A isolated from E. coli strain WD101 (Figure 6; right lane)38. WD101 produces lipid A heavily modified with aminoarabinose (L-Ara4N) and phosphoethanolamine (pEtN). Since both 1- and 4‘-phosphates are available for modification, lipid A from WD101 can be described as singly modified, containing only one L-Ara4N or pEtN at either phosphate, or doubly modified where both phosphates are modified in a combinatorial manner. In addition to modification at the 1- and 4‘- phosphates, palmitate addition is also observed (see Figure 1) and increases the Rf value of lipid A species in this solvent system (Figure 6). If desired, densitometry analysis using a phosphorimager, can be used to quantifiably estimate relative amounts of lipid A species within the same sample .
Figure 1. Representative lipid A domain structures from E. coli K-12 and S. enterica serovar Typhimurium. Modifications to the conserved lipid A structure are shown (right), as described in Representative Results. Click here to view larger figure.
Figure 2. Schematic of lipid A isolation procedure. Outline depicts chemical lysis of bacterial cell pellet using single phase Bligh-Dyer mixture, centrifugation of lysate to pellet LPS, mild-acid hydrolysis to liberate lipid A from attached polysaccharide, and final purification of lipid A using two phase Bligh-Dyer extraction. Click here to view larger figure.
Figure 3. MALDI-MS analysis of lipid A isolated from E. coli K-12 (W3110). Spectra obtained from the average of >300 shots. Singly charged [M-H]– lipid A is observed as the molecular ion at m/z 1,796.2, which corresponds to a deprotonated species of the structure shown at right.
Figure 4. ESI-MS analysis of lipid A isolated from E. coli K-12 (W3110). Singly [M-H] and doubly-charged [M-2H]2- lipid A species are observed as molecular ions of m/z 1,796.2 and m/z 898.1, respectively.
Figure 5. MS/MS analysis of lipid A isolated from E. coli K-12 (W3110). Collision induced dissociation (A) or ultraviolet photodissociation (B) were used to fragment the precursor ion m/z 1,796.2. UVPD specific product ions are indicated in red. A fragmentation map is provided (C), where black dashed lines indicate fragmentation associated with both CID and UVPD, and red dashed lines indicate UVPD specific fragmentation. Values listed beneath the fragmentation map correspond to exact masses of [M-H]– product ions. Click here to view larger figure.
Figure 6. TLC-based separation of lipid A species isolated from E. coli K-12. 32P-labeled lipid A was isolated from W3110 (left lane) or WD101 (right lane) and separated in a TLC tank solvent system containing chloroform:pyridine:88% formic acid:water (50:50:16:5 v/v).
In this protocol we have detailed the isolation of lipid A species from whole cells of bacteria, and described TLC or MS based analytical methods to chemically characterize this isolated material. Tandem mass spectrometry is a powerful strategy for de novo structural characterization of biological compounds, and is invaluable for the chemical characterization of the panoply of lipid A molecules observed in nature. CID and UVPD are two complementary activation methods that create different types of product ions that provide key fingerprints for lipid A molecules. MS/MS fragmentation using both CID and UVPD allows elucidation of subtle differences of lipid A structures, providing finer detail for chemical structure assignments. Data of this type are necessary to establish precise correlate structure/function relationships in the biology of lipid A molecular species. We have also described the procedure for 32P-radiolabeling lipid A species in small-scale bacterial cultures, where the chemical pattern of 32P-lipid A species can be visualized using TLC and autoradiography.
There are a number of features to this protocol that any user should be aware of. For large-scale lipid A preparations (protocol 1), the proportion of starting solvent to amount of bacterial pellet can be optimized to improve overall yield. However this proportion can only be determined empirically. The amounts described in this protocol represent a good starting point for most bacterial strains. Culture volumes for lipid A extraction and isolation can also be adjusted depending on the bacterial strain you are working with. For instance, V. cholerae requires at least 200 ml of culture in order to obtain high quality mass spectra; however, the culture volume for E. coli can be scaled down to 5 ml. More starting material (larger culture volumes) is required for some bacterial species because the hydrolysis step that releases lipid A from whole LPS is less efficient. For example organisms containing a functional Kdo dioxygenase or Kdo kinase exhibit decreased lipid A yields after mild-acid hydrolysis39. Often, mutants with altered LPS/lipid A structures or a particular bacterial species are often difficult to pellet during cell harvest. For these strains, the length of centrifugation can be extended to increase yield. Also of note, after cell lysis in a single-phase Bligh-Dyer mixture and LPS is pelleted (see step 1.9), additional wash steps may be required to reduce phospholipid contamination. When isolating lipid A from E. coli or Salmonella, only one wash is required. However, if isolating lipid A from other organisms (e.g. V. cholerae or Helicobacter pylori), additional wash steps are required.
After mild acid hydrolysis in SDS, the yield of lipid A species with reduced hydrophobicity (i.e. more phosphate groups >2 or fewer acyl chains <5) can be improved by using an acidic Bligh-Dyer extraction. For the volumes used in Protocol section 1, add 225 μl of concentrated HCl to the SDS solution containing hydrolyzed lipid A followed by 30 ml of chloroform and 30 ml of methanol for a two phase Bligh-Dyer mixture of chloroform:methanol: 0.1 M HCl (2:2:1.8, v/v). For the volumes used in Protocol section 6 add 15 μl of concentrated HCl to the SDS solution containing hydrolyzed lipid A followed by 2 ml of chloroform and 2 ml of methanol yielding a chloroform: methanol: 0.1 M HCl (2:2:1.8, v/v) mixture. After an acidic Bligh-Dyer extraction, pyridine can be added to the pooled lower phases to neutralize the acid (1 drop of pyridine/2 ml of final sample volume). This additional step should be performed before drying the sample, in a chemical fume hood. Be careful not to use excess pyridine, which can lead to the removal of ester-linked fatty acids. Additionally, if the lipid sample is difficult to dry under nitrogen, add a few milliliters of chloroform:methanol (4:1, v/v) to the flask and continue to dry the sample to completion.
The complex chemical heterogeneity of lipid A species observed in some organisms (e.g. V. cholerae, Yersinia pseudotuberculosis) can sometimes make TLC- or MS-based analysis difficult. Column chromatography can be employed upstream of these analytical techniques to pre-fractionate isolated lipid A species into more simple mixtures. Anion exchange with diethylaminoethyl (DEAE)-cellulose is most commonly used40. As a general guideline lipid A modified at either phosphate position, with non-acidic groups such as aminoarabinose or phosphoethanolamine, elutes before unmodified lipid A species40. Similarly tris-phosphorylated lipid A elutes well after unmodified bisphosphorylated species36,40. Reverse phase chromatography can be used to fractionate lipid A species of varying degrees of hydrophobicity41. Column chromatography is also useful in the removal of residual SDS after mild acid hydrolysis and subsequent Bligh-Dyer lipid A extraction steps. High levels of residual SDS can contribute to signal suppression in spectra obtained by our sensitive ESI-MS protocols.
The authors have nothing to disclose.
This work was supported by Grants AI064184 and AI76322 from the National Institutes of Health (NIH) and by Grant 61789-MA-MUR from the Army Research Office to M.S.T. Research was also supported by Welch Foundation Grant F1155 and NIH grant R01GM103655 to J.S. B.
Name of Reagent/Material | Company | Catalog Number | Comments |
Chloroform | Thermo Fisher Scientific | C607 | HPLC Grade |
Methanol | Thermo Fisher Scientific | A452 | HPLC Grade |
Teflon FEP Centrifuge Bottles | Thermo Fisher Scientific | 05-562-21 | |
Silica Gel 60 TLC Plates | EMD Biosciences | 5626-6 | |
Grade No. 3MM Chromatography Paper | Whatman | 3030700 | |
Orbitrap Elite | Thermo Fisher Scientific | ||
Mass Spectrometer | |||
ExciStar XS Excimer Lasrer | Coherent Inc. | ||
PicoTip Nanospray ESI emitters | New Obectives | ≥ 30 μm to reduce clogging | |
Model 505 Pulse/Delay Generator | Berkeley Nucleonics Corporation | ||
Hot Plate Thermoylne 2200 | Barnstead/Thermolyne | HPA2235MQ | |
16×125 mm GPI 15-415 Threaded Disposable Borosilicate Culture Tubes | Corning Pyrex | 99449-16X | |
Reusable Threaded PTFE screw caps GPI 45-415 | Corning | 9999-152 | |
Personal Molecular Imager System (phosphorimager) | BioRad | 170-9400 | |
Autoradiography Cassette | Thermo Fisher Scientific | FBCS810 | |
Phosphorscreen SO230 | Kodak | ||
Peptide Mass Standards Kit | Sequazyme | P2-3143-00 | |
Sonifier S250-A | Branson | 101063196 | |
1.5 ml 12×32 mm Tapered Base Screw Thread Vial | Thermo Fisher Scientific | C4000-V1 |