Name: enrichment of bacterial lipoproteins and preparation of n-terminal lipopeptides for structural determination by mass spectrometry
Uploaded: 2018-05-21T12:30:00
Description: Watch this Scientific Journal Video about Enrichment of Bacterial Lipoproteins and Preparation of N-terminal Lipopeptides for Structural Determination by Mass Spectrometry at JoVE.com

Research in the Meredith lab was supported by startup funds provided by the Eberly College of Science (Pennsylvania State University). We thank Dr. Tatiana Laremore for expert technical advice and access to equipment at the Penn State Proteomics and Mass Spectrometry Core Facility, University Park, PA, where mass spectrometric analyses were performed.

1. Cell Growth and Lysis
<ol>
	<li>Grow bacteria in 15 mL tryptic soy broth (TSB) or similar rich media to late exponential phase (OD600 of 1.0 - 1.5). Harvest cells by centrifugation, wash once with Tris-buffered saline/EDTA (TBSE) and continue with protocol or freeze until use. 
	NOTE: TBSE: 20 mM Tris-hydrochloride (HCl), pH 8.0, 130 mM sodium chloride (NaCl), and 5 mM ethylenediaminetetraacetic acid (EDTA)). Lipoprotein expression and modification can be influenced by growth conditions (e.g.</em...

<ol>
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The protocol herein describes two distinct stages of lipoprotein characterization: enrichment by TX-114 phase partitioning and structural determination by MALDI-TOF MS. During TX-114 extraction, additional centrifugation removes contaminating proteins that precipitate during this process, followed by acetone precipitation to yield highly enriched lipoproteins. By limiting the scale of each preparation to 15-mL worth of cells, several samples can be easily processed in parallel, and if desired, pooled at the end of the pr...

Bacterial lipoproteins are characterized by a conserved N-terminal lipid-modified cysteine that anchors the globular protein domain to the cell membrane surface. They are universally distributed in bacteria, constituting 2 to 5% of all cellular genes within a typical genome1. Lipoproteins play critical roles in a wide variety of cellular processes, including nutrient uptake, signal transduction, assembly of protein complexes, and in maintaining cell envelope structural integrity2. In pathogenic bacteria, lipoproteins serve as virulence factors3,4. During an infection, recognition of N-terminal lipopeptides by Toll-like receptor (TLR) 2 incites an innate immune response to remove invading pathogens. Depending on the N-terminal acylation state, lipoproteins are generally recognized by alternate TLR2 heterodimeric complexes. TLR2-TLR1 recognizes N-acylated lipopeptides, while TLR2-TLR6 binds free lipopeptide &#945;-amino termini. Once bound, the signaling pathways converge to induce secretion of proinflammatory cytokines3,4.
It was previously thought that lipoproteins from Gram-positive bacteria were diacylated and those from Gram-negative bacteria were triacylated, differing in the absence or presence of an amide-linked fatty acid on the conserved N-terminal cysteine residue. This assumption was supported by the lack of sequence orthologs in Gram-positive genomes to Lnt, the Gram-negative N-acyl transferase that forms triacylated lipoproteins5. However, recent studies have revealed lipoprotein triacylation in Gram-positive Firmicutes that lack lnt, as well as three novel N-terminal lipoprotein structures, termed the peptidyl, lyso, and N-acetyl forms6,7,8. These findings raise questions about possible yet-to-be-discovered lipoprotein forms, alongside fundamental questions about how these novel lipoproteins are made and what physiological purpose or advantage the various forms impart. Furthermore, they clearly demonstrate the current inability of genomics to predict lipoprotein structure. Indeed, we recently identified a novel class of lipoprotein N-acyl transferases, called Lit, from Enterococcus faecalis and Bacillus cereus that makes lyso-form lipoproteins9. This indicates the need to experimentally verify lipoprotein structure, which can be challenging due to their extremely hydrophobic nature and limited methods available to characterize their molecular structure.
To facilitate studies on lipoprotein induction of the host immune response, as well as N-terminal structural determination, we have adapted several previously-described protocols in order to purify bacterial lipoproteins and prepare the N-terminal tryptic lipopeptides for analysis by MALDI-TOF MS6,10,11,12. Lipoproteins are enriched using an established Triton X-114 (henceforth referred to as surfactant or TX-114) phase partitioning method, with optimization to remove contaminating non-lipoproteins and increase lipoprotein yield. These lipoproteins are suitable for direct use in TLR assays or for further purification by SDS-PAGE. For MALDI-TOF MS, transfer of the lipoproteins to nitrocellulose membrane provides a scaffold for efficient in situ trypsin digestion, washing, and subsequent elution from the membrane surface, resulting in highly purified N-terminal lipopeptides. Nitrocellulose has been shown to facilitate sample handling and improve sequence coverage for highly hydrophobic peptides from integral membrane proteins13,14, as well as lipoproteins9,10. The method has the additional advantage of fractionating peptides based on polarity, so that intermediate wash solutions can be analyzed for high confidence protein identification simultaneously with N-terminal structural determination in a single experiment. This protocol uniquely features intentional sodium adduct formation to promote parent ion fragmentation towards dehydroalanyl ions during MS/MS, aiding in structural assignment of the N-acylation state. The N-terminus is both the most variable and key feature related to TLR recognition of lipoproteins. Taken together, this protocol has allowed intensive and reproducible studies on lipoproteins, with the individual stages of purification and structural determination by MALDI-TOF MS easily adapted depending on the overall goal of the experiment.

<table>
	<tbody>
		<tr>
			<td>Materials</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>0.01 mm Zirconia/silica beads</td>
			<td>BioSpec Products</td>
			<td>110791012</td>
			<td></td>
		</tr>
		<tr>
			<td>Acetic acid</td>
			<td>EMD</td>
			<td>AX0073-9</td>
			<td></td>
		</tr>
		<tr>
			<td>Acetone</td>
			<td>EMD</td>
			<td>AX0116-6</td>
			<td></td>
		</tr>
		<tr>
			<td>Acetonitrile</td>
			<td>EMD</td>
			<td>AX0142-6</td>
			<td></td>
		</tr>
		<tr>
			<td>Ammonium bicarbonate</td>
			<td>Fluka Analytical</td>
			<td>09830</td>
			<td></td>
		</tr>
		<tr>
			<td>BioTrace NT Nitrocellulose</td>
			<td>PALL Life Sciences</td>
			<td>66485</td>
			<td></td>
		</tr>
		<tr>
			<td>Bovine serum albumin (BSA) digest standard</td>
			<td>Protea</td>
			<td>PS-204-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Chloroform</td>
			<td>Acros Organics</td>
			<td>423550025</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethylenediaminetetraacetic acid (EDTA)</td>
			<td>Fisher Scientific</td>
			<td>BP118</td>
			<td></td>
		</tr>
		<tr>
			<td>HPLC Grade water</td>
			<td>EMD</td>
			<td>WX0008-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Lysozyme</td>
			<td>Fisher Scientific</td>
			<td>BP535-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Methanol</td>
			<td>Sigma-Aldrich</td>
			<td>34860</td>
			<td></td>
		</tr>
		<tr>
			<td>Phenylmethyl sulfonyl fluoride (PMSF)</td>
			<td>Amresco</td>
			<td>0754</td>
			<td></td>
		</tr>
		<tr>
			<td>Pierce trypsin protease</td>
			<td>Thermo Scientific</td>
			<td>90057</td>
			<td></td>
		</tr>
		<tr>
			<td>Ponceau S</td>
			<td>Acros Organics</td>
			<td>161470100</td>
			<td></td>
		</tr>
		<tr>
			<td>Protein LoBind Tube 0.5mL</td>
			<td>Eppendorf</td>
			<td>022431064</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium bicarbonate</td>
			<td>Sigma-Aldrich</td>
			<td>792519</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium chloride</td>
			<td>Macron Fine Chemicals</td>
			<td>7581-06</td>
			<td></td>
		</tr>
		<tr>
			<td>Trifluoroacetic acid (TFA)</td>
			<td>Sigma-Aldrich</td>
			<td>299537</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris-hydrochloride (HCl)</td>
			<td>Fisher Scientific</td>
			<td>BP152</td>
			<td></td>
		</tr>
		<tr>
			<td>Triton X-114</td>
			<td>Sigma-Aldrich</td>
			<td>93422</td>
			<td></td>
		</tr>
		<tr>
			<td>Tryptic soy broth (TSB)</td>
			<td>BD</td>
			<td>211822</td>
			<td></td>
		</tr>
		<tr>
			<td>&#945;-cyano-4-hydroxycinnamic acid (MS Grade)</td>
			<td>Sigma-Aldrich</td>
			<td>C8982</td>
			<td></td>
		</tr>
		<tr>
			<td>Name</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Comments</td>
		</tr>
		<tr>
			<td>Equipment</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>MagNALyser</td>
			<td>Roche</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Trans-Blot Turbo Transfer System</td>
			<td>Bio-Rad</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>MALDI-TOF target</td>
			<td>Bruker Daltonics</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Ultraflextreme MALDI-TOF-TOF</td>
			<td>Bruker Daltonics</td>
			<td></td>
			<td>Equipped with a 355 nm frequency-tripled Nd:YAG smartbeam-II laser</td>
		</tr>
	</tbody>
</table>

enrichment of bacterial lipoproteins and preparation of n-terminal lipopeptides for structural determination by mass spectrometry

Lipoproteins are important constituents of the bacterial cell envelope and potent activators of the mammalian innate immune response. Despite their significance to both cell physiology and immunology, much remains to be discovered about novel lipoprotein forms, how they are synthesized, and the effect of the various forms on host immunity. To enable thorough studies on lipoproteins, this protocol describes a method for bacterial lipoprotein enrichment and preparation of N-terminal tryptic lipopeptides for structural determination by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Expanding on an established Triton X-114 phase partitioning method for lipoprotein extraction and enrichment from the bacterial cell membrane, the protocol includes additional steps to remove non-lipoprotein contaminants, increasing lipoprotein yield and purity. Since lipoproteins are commonly used in Toll-like receptor (TLR) assays, it is critical to first characterize the N-terminal structure by MALDI-TOF MS. Herein, a method is presented to isolate concentrated hydrophobic peptides enriched in N-terminal lipopeptides suitable for direct analysis by MALDI-TOF MS/MS. Lipoproteins that have been separated by Sodium Dodecyl Sulfate Poly-Acrylamide Gel Electrophoresis (SDS-PAGE) are transferred to a nitrocellulose membrane, digested in situ with trypsin, sequentially washed to remove polar tryptic peptides, and finally eluted with chloroform-methanol. When coupled with MS of the more polar trypsinized peptides from wash solutions, this method provides the ability to both identify the lipoprotein and characterize its N-terminus in a single experiment. Intentional sodium adduct formation can also be employed as a tool to promote more structurally informative fragmentation spectra. Ultimately, enrichment of lipoproteins and determination of their N-terminal structures will permit more extensive studies on this ubiquitous class of bacterial proteins.

A schematic of the protocol is provided in Figure 1. The lipoprotein-enriched fraction extracted from Enterococcus faecalis ATCC 19433 by TX-114 is shown in Figure 2. For comparison, the banding pattern of the precipitated protein fraction is also shown. Proteins from this fraction were confirmed by MALDI-MS to be highly abundant contaminating proteins other than lipoproteins (Table 1). The mass spectra ...

Watch this Scientific Journal Video about Enrichment of Bacterial Lipoproteins and Preparation of N-terminal Lipopeptides for Structural Determination by Mass Spectrometry at JoVE.com

Enrichment of Bacterial Lipoproteins and Preparation of N-terminal Lipopeptides for Structural Determination by Mass Spectrometry

The enrichment of bacterial lipoproteins using a non-ionic surfactant phase partitioning method is described for direct use in TLR assays or other applications. Further steps are detailed to prepare N-terminal tryptic lipopeptides for structural characterization by mass spectrometry.

Lipoproteins are important constituents of the bacterial cell envelope and potent activators of the mammalian innate immune response. Despite their ...

The overall goal of this procedure is to extract lipoproteins from bacterial cells for direct applications and to further prepare N-terminal lipopeptides for structural analysis by MALDI-TOF mass spectrometry. This method can help answer key questions in the immunology field, as the lipoproteins'N-terminal structure influences Toll-like receptor recognition and signaling, impacting the host's immune response. The unique advantage of this technique is the optional but intentional formation of sodium adducts, which promotes fragmentation towards the diagnostic dehydroalanyl ion, aiding in structural assignment of the lipoprotein's acylation state.Grow bacteria in 15 milliliters of tryptic soy broth or similar rich media to late exponential phase. Harvest the cells by centrifugation before washing once with Tris-buffered saline EDTA or TBSE. resuspend the cells in 800 microliters of TBSE with one millimolar PMSF and 0.5 milligram per milliliter lysozyme.Transfer the solution to a 2.0-milliliter threaded microcentrifuge tube with screw cap and O-ring prior to incubating for 20 minutes at 37 degrees Celsius. Add approximately 800 microliters of 0.1 millimeter zirconia silica beads to the tube, then disrupt the cells by shaking at maximum speed on a homogenizer for five cycles of 30 seconds each with a two-minute rest on ice between each cycle. Centrifuge the sample at 3, 000 times g for five minutes at four degrees Celsius to pellet beads and unbroken cells.Transfer the supernatant to a new 2.0-milliliter microcentrifuge tube, then keep on ice. Add 200 microliters of TBSE to the remaining pellet and return to the homogenizer for an additional cycle. Centrifuge as before and combine the supernatant with the previous supernatant.Supplement the supernatant with TX-114 surfactant to a final concentration of 2%by adding an equal volume of 4%surfactant in ice-cold TBSE. Incubate the supplemented supernatant on ice for one hour, mixing by inversion every 15 minutes. Transfer the tube to a 37-degrees Celsius water bath, and incubate for 10 minutes to induce phase separation.Centrifuge the sample at 10, 000 times g for 10 minutes at room temperature to maintain biphasic separation. Gently pipette off the upper aqueous phase and discard. Add ice-cold TBSE to the lower surfactant phase to refill the tube to its original volume and invert to mix.Incubate on ice for 10 minutes. Following incubation, transfer the tube to a 37-degrees Celsius water bath and incubate for 10 minutes to induce phase separation, then centrifuge at 10, 000 time g for 10 minutes at room temperature. After repeating these steps once more for a total of three separations, remove the upper aqueous phase and discard.Remove the pellet of precipitated proteins that formed during the course of the extractions by adding one volume of ice-cold TBSE to the surfactant phase. Centrifuge at four degrees Celsius and 16, 000 times g for two minutes to pellet the insoluble protein. Immediately transfer the supernatant to a fresh 2.0-milliliter microcentrifuge tube containing 1, 250 microliters of 100%acetone.Mix the sample by inversion and incubate overnight at minus 20 degrees Celsius to precipitate the protein. The next day, centrifuge the sample at 16, 000 times g for 20 minutes at room temperature to pellet the lipoproteins with attention to the orientation of the tube. Wash the pellet twice with 100%acetone before decanting the acetone and allowing the sample to air dry.Then, add 20 to 40 microliters of 10-millimolar Tris-HCL, pH 8.0, and thoroughly resuspend the pellet by pipetting up and down against the wall with the precipitated lipoproteins. Separate the lipoproteins by SDS-PAGE using standard methods. Transfer the lipoproteins to a nitrocellulose transfer membrane using a standard electro blotting procedure.Transfer the nitrocellulose membrane to a container and cover with Ponceau S solution. Rock gently for five minutes or until red-pink bands are visible. Pour off Ponceau S solution and carefully rinse the nitrocellulose membrane with distilled water to remove excess stain.With a clean razor blade, excise the desired band and transfer to a microcentrifuge tube. Wash the membrane three times with one milliliter of distilled water to completely de-stain the band. After transferring the section to a clean surface, use a clean razor blade to dice the nitrocellulose strip into small pieces of approximately one millimeter by one millimeter.Collect the pieces into a 0.5-milliliter low protein binding microcentrifuge tube. Finally, wash the pieces twice with 500 microliters of freshly-prepared 50-millimolar ammonium bicarbonate, pH 7.8, in a HPLC-grade water. Resuspend the nitrocellulose pieces in 20 microliters of a 20-microgram per milliliter solution of Trypsin in 50-millimolar ammonium bicarbonate.Vortex the resuspended nitrocellulose pieces to mix. Then spin the tube briefly to ensure that all pieces are fully covered by the Trypsin solution. Cover the tube lid using paraffin film to prevent evaporation and incubate the digest overnight at 37 degrees Celsius.Spin the sample at 16, 000 times g for 30 seconds and remove the liquid by pipetting. Then, add 50 microliters of 0.5%trifluoroacetic acid in HPLC-grade water. After vortexing to mix, spin the sample briefly to ensure all pieces are covered by the solution and incubate the sample for 10 minutes at room temperature.Following removal of the liquid by pipetting, repeat this step with 50 microliters of 10%acetonitrile, and then repeat again with 50 microliters of 20%acetonitrile. To elute the tightly-bound lipopeptides, add 15 microliters of freshly-made 10 milligrams per milliliter CHCA matrix dissolved in chloroform-methanol. Incubate for 10 minutes at room temperature with intermittent vortexing.To promote sodium adduct formation, supplement the solution of CHCA in chloroform-methanol with aqueous sodium bicarbonate to a final concentration of one millimolar. After spinning the sample briefly, use a pipette to carefully transfer the liquid to a new low protein binding microcentrifuge tube. This solution will contain the bulk of the N-terminal lipopeptides.Deposit one microliter of the eluted lipopeptides with CHCA onto a polished steel MALDI target. Immediately proceed to mass spectrometry. Example mass spectra of the stepwise nitrocellulose wash solutions of the enterococcus faecalis lipoprotein PnrA are shown here.With each subsequent wash, changes in signal intensity and a decrease in individual peaks are observed, culminating in the highly-enriched N-terminal lipopeptide ion in the final elution fraction. MS/MS spectrum of the parent lipopeptide ion reveals that it is the lysoform, with fragment ions corresponding to the N-terminal PnrA tryptic peptide featuring an alpha-amino linked acyl chain and a monoacylglycerol structure. Addition of sodium bicarbonate to the eluted lipopeptide fraction of the Escherichia coli lipoprotein Lpp results in a 22-Dalton increase from the calculated N-terminal mass.MS/MS analysis of the parent ion versus its sodium adduct demonstrates preferential fragmentation towards the dehydroalanyl ion of the sodiated parent through neutral elimination of the diaco thioglyceryl moiety. This aids in structural determination of the N-terminal acylation state. While carrying out this procedure, it is worthwhile to remember that each stepwise nitrocellulose wash fraction can be analyzed by mass spectrometry, allowing for both protein identification and N-terminal characterization of the lipopeptide in a single experiment.Following lipoprotein extraction from bacteria, other experiments such as cell-based assays measuring Toll-like receptor signaling can be performed to answer additional questions like how the lipoprotein acylation state influences the host's immune response.

Research

JoVE Journal

Immunology and Infection

Invasion of Human Cells by a Bacterial Pathogen

Here we will describe how we study the invasion of human endothelial cells by bacterial pathogen Staphylococcus aureus . The general protocol can be ...

Structure of HIV-1 Capsid Assemblies by Cryo-electron Microscopy and Iterative Helical Real-space Reconstruction

Cryo-electron microscopy (cryo-EM), combined with image processing, is an increasingly powerful tool for structure determination of macromolecular protein ...

Saliva, Salivary Gland, and Hemolymph Collection from Ixodes scapularis Ticks

Saliva, Salivary Gland, and Hemolymph Collection from Ixodes scapularis Ticks

Ticks are found worldwide and afflict humans with many tick-borne illnesses. Ticks are vectors for pathogens that cause Lyme disease and tick-borne ...

Discovery of New Intracellular Pathogens by Amoebal Coculture and Amoebal Enrichment Approaches

Intracellular pathogens such as legionella, mycobacteria and Chlamydia-like organisms are difficult to isolate because they often grow poorly or not at ...

Rapid Identification of Gram Negative Bacteria from Blood Culture Broth Using MALDI-TOF Mass Spectrometry

An important role of the clinical microbiology laboratory is to provide rapid identification of bacteria causing bloodstream infection. Traditional ...

Preparation of a Blood Culture Pellet for Rapid Bacterial Identification and Antibiotic Susceptibility Testing

Bloodstream infections and sepsis are a major cause of morbidity and mortality. The successful outcome of patients suffering from bacteremia depends on a ...

Electroporation of Functional Bacterial Effectors into Mammalian Cells

The study of protein interactions in the context of living cells can generate critical information about localization, dynamics, and interacting partners. ...

Generation and Multi-phenotypic High-content Screening of Coxiella burnetii Transposon Mutants

Generation and Multi-phenotypic High-content Screening of Coxiella burnetii Transposon Mutants

Invasion and colonization of host cells by bacterial pathogens depend on the activity of a large number of prokaryotic proteins, defined as virulence ...

Alternative In Vitro Methods for the Determination of Viral Capsid Structural Integrity

Alternative In Vitro Methods for the Determination of Viral Capsid Structural Integrity

Human norovirus exacts considerable public health and economic losses worldwide. Emerging in vitro cultivation advances are not yet applicable for routine ...

Identification of Nucleolar Factors During HIV-1 Replication Through Rev Immunoprecipitation and Mass Spectrometry

The HIV-1 infectious cycle requires viral protein interactions with host factors to facilitate viral replication, packaging, and release. The infectious ...