Name: expression, purification, and antimicrobial activity of s100a12
Uploaded: 2017-05-13T13:00:00.000+00:00
Duration: 11 min 10 s
Description: Watch this Scientific Journal Video about Expression, Purification, and Antimicrobial Activity of S100A12 at JoVE.com

This research was supported by the Department of Veterans Affairs Career Development Award 1IK2BX001701, CTSA award UL1TR000445 from the National Center for Advancing Translational Sciences, the National Science Foundation Award Numbers 1547757 and 1400969, and NIH grant GM05551. Its contents are solely the responsibility of the authors and do not necessarily represent official views of the National Center for Advancing Translational Sciences or the National Institutes of Health.

1. Expression of S100A12
<ol>
	<li>Transform competent BL21 DE3 cells with a pGEMEX-S100a12 plasmid using a standard heat shock protocol18. Add 1 to 5 &#181;L of plasmid to 50 &#181;L of bacteria in a microcentrifuge tube on ice. Incubate for 20 min.</li>
	<li>Heat shock the cells at 42 &#176;C for 30 s.</li>
	<li>Incubate the cells on ice for 2 min.</li>
	<li>Add 500 &#181;L of SOC media to the cells. Incubate at 37 &#176;C with shaking at 250 rpm on an orbital shaker for 1 h.</li>
	<li>Plate 150 &#181;L of the transformation reaction on LB-agar medium (supplemented with 100 &#181;g/mL ampicillin). Incubate for 12-16 h at 37 &#176;C.</li>
	<li>Pick one colony. Inoculate 2 mL of LB (supplemented with 100 &#181;g/mL ampicillin).</li>
	<li>Incubate for 4-6 h at 37 &#176;C on an orbital shaker (300 rpm). The OD600 should read between 1-3 absorbance units.</li>
	<li>Add 500 &#181;L of starter culture to 50 mL of ZYM-5052 autoinduction media26 supplemented with 100 &#181;g/mL of ampicillin. For best aeration and maximum expression, use a 250 mL baffled Erlenmeyer flask. Shake (300 rpm) for 24 h, at 37 &#176;C.</li>
	<li>Transfer bacterial suspension to a centrifuge tube. Pellet the cells by centrifugation (4,000 x g, 10 min) at 4 &#176;C.</li>
	<li>Decant the media, log sample, and store cell paste at -80 &#176;C. Sample is stable for years.</li>
</ol>
2. Purification of S100A12 Using Low Pressure Chromatography
<ol>
	<li>Resuspend cells in 30 mL of 20 mM Tris, pH 8.0.</li>
	<li>Sonicate the suspension on ice to lyse cells. Use ~20 W output, 5 s on and 5 s off cycle for 5 min.</li>
	<li>Transfer the solution to high-speed centrifuge tubes. Clarify the cell lysate by centrifugation, 20,000 x g for 30 min at 4 &#176;C.</li>
	<li>Decant the supernatant and transfer to a clean 100 mL polypropylene beaker. Cool the solution by placing the beaker on ice. Add a stir bar and slowly add 11.20 g of ammonium sulfate. Allow the solution to stir on ice for an additional 1 h. This will create a 60% solution of ammonium sulfate and precipitate most of the E. coli endogenous proteins. S100A12 will remain soluble.</li>
	<li>Centrifuge the solution at 4 &#176;C, 20,000 x g for 20 min to pellet the precipitated protein.</li>
	<li>Decant the supernatant and transfer to dialysis tubing (MWCO 3,500 kDa). Dialyze against 1 L of 20 mM Tris, pH 8.0 at 4 &#176;C. Change the dialysis buffer twice. Allow 4 h in between changes.</li>
	<li>Anion exchange chromatography
	<ol>
		<li>Perform chromatography on a low pressure system. Typical flow rate is 1 mL/min.</li>
		<li>Equilibrate a 5 mL Sepharose column with 10 mL of 20 mM Tris, pH 8.0.</li>
		<li>Load the ~40 mL of S100A12 solution using the sample pump (collect the flow through).</li>
		<li>Wash the column with 10 mL of 20 mM Tris, pH 8.</li>
		<li>Develop the column with a 0-30% gradient (Buffer B is 20 mM Tris, pH 8.0, 1 M NaCl) over 19 column volumes (CV, 95 mL). Collect 5 mL fractions.</li>
		<li>Take a 10 &#181;L aliquot of each fraction and analyze using MES SDS PAGE with Coomassie staining. Run gel using constant voltage (20 V/cm) for 30 min.</li>
		<li>Pool fractions containing S100A12. S100A12 runs at ~10 kDa protein on a denaturing gel.</li>
		<li>Concentrate fractions to 5 mL using an ultrafiltration device (MWCO 10 kDa). Centrifuge at 3,000 x g for ~8 min. Take the top fraction.</li>
	</ol>
	</li>
	<li>Size-exclusion chromatography
	<ol>
		<li>Equilibrate S75 column with 1 CV (120 mL) of 20 mM Tris pH 8, 100 mM NaCl.</li>
		<li>Inject &#60; 5 mL of concentrated S100A12 fractions (from the ion exchange chromatography).</li>
		<li>Develop the column at a flow rate of 1 mL/m over 120 mL. Collect 5 mL fractions.</li>
		<li>Take a 10 &#181;L aliquot of each fraction and analyze using SDS PAGE with Coomassie staining. Validate protein identity using western blot or mass spectrometry (calculated molecular mass of monomeric subunit 10,575.0 Da, measured 10575.4 Da).</li>
	</ol>
	</li>
	<li>Pool fractions
	<ol>
		<li>Measure the absorbance of the protein A280 using a spectrophotometer. Use the SEC buffer as a blank. The calculated extinction coefficient for S100A12 homodimer is 5960 M-1 cm-1. 
		NOTE: Typical yields are 35-45 mg of S100A12 per 50 mL of culture.</li>
		<li>Aliquot S100A12 into 1.5 mL microcentrifuge tubes (1 mg/tube), flash freeze in liquid nitrogen and store at -80 &#176;C.</li>
	</ol>
	</li>
</ol>
3. Antimicrobial Activity Assays
<ol>
	<li>Streak H. pylori strain G27 onto tryptic soy agar plates supplemented with 5% sheep blood (blood agar plates). Grow 2-3 days at 37 &#176;C in room air supplemented with 5% carbon dioxide.</li>
	<li>Inoculate H. pylori into Brucella broth supplemented with 1x cholesterol. Culture overnight shaking (250 rpm) at 37 &#176;C in room air supplemented with 5% carbon dioxide.</li>
	<li>Dilute H. pylori 1:10 into 50% Brucella broth, 50% calprotectin buffer plus 1x cholesterol and culture in medium alone or supplemented with 100 &#181;M zinc chloride plus 0, 100 or 1,000 &#181;g/mL of purified S100A12. Culture overnight shaking (250 rpm) at 37 &#176;C in room air supplemented with 5% carbon dioxide.</li>
	<li>The following day, perform serial dilutions and plate onto blood agar plates. Allow bacterial colonies to grow for 2-3 days at 37 &#176;C in room air supplemented with 5% carbon dioxide. Enumerate the colony forming units to calculate bacterial growth in the presence or absence of S100A12 and/or exogenous zinc.</li>
</ol>

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The authors declare that they have no competing financial interests.

An efficient protocol for both expression and purification of human S100A12 is presented. The E. coli expression system is the most common tool used for the production of recombinant proteins, particularly when mg quantities are required for biochemical and biophysical studies. A key enhancement of the procedure described here is the use of auto-induction media26 which increases the yield of purified protein by a factor of almost thirty as compared to expression with standard Luria-broth ...

S100 proteins are a class of the EF-hand family of calcium binding proteins with a diverse array of functions1. They are expressed in a tissue and cell specific manner, and regulate a broad spectrum of cellular functions2,3. Unique to calcium binding proteins, S100 proteins exhibit both intracellular and extracellular functions4,5. Within the cell, Ca2+ binding induces a conformational change that exposes a hydrophobic surface that specifically targets protein binding partners6. This intracellular mechanism regulates important processes such as cell proliferation, differentiation and energy metabolism. In the extracellular milieu, S100 proteins exhibit two functions7. In one, they act as damage associated molecular pattern (DAMP) proteins and initiate a pro-inflammatory immune response through interaction with pattern recognition receptors8,9. Additionally, several members of the S100 protein class sequester transition metals, a function that serves to starve microbial pathogens in a process termed nutritional immunity10,11.
S100A12 (also known as calgranulin C and EN-RAGE) is highly expressed in macrophages and neutrophils and has been identified as a potential biomarker for inflammatory diseases12,13. In addition to binding calcium at its EF-Hand sites, S100A12 has two high affinity transition metal binding sites located at opposite ends of the dimer interface14,15. Each binding site is comprised of three histidine residues and one aspartic acid residue and can chelate zinc or copper16,17. Recently, we reported that S100A12-dependent zinc starvation is important in regulating Helicobacter pylori growth and the activity of pro-inflammatory virulence factors18.
H. pylori infects the stomach of about half of the world&#39;s human population; making it arguably one of the most successful bacterial pathogens19. Infection with H. pylori can lead to significant gastric disease outcomes including gastritis, peptic and duodenal ulcer, mucosa associated lymphoid tissue (MALT) lymphoma, and invasive gastric adenocarcinoma (stomach cancer). Stomach cancer is the leading cause of non-cardia cancer-associated death in the world, and the single biggest associated risk factor for stomach cancer is infection with H. pylori.
H. pylori persists in the gastric niche despite a robust immune response to the pathogen, underscoring the need for a better understanding of immune mechanisms of controlling this bacterial infection20,21,22,23. H. pylori-associated inflammation is characterized by a profound infiltration of polymorphonuclear cells, or neutrophils, which deposit a repertoire of antimicrobial proteins, including S100A12, at the site of infection18,24,25. In an effort to understand the complex dialogue between host and pathogen, we sought to refine the technique to purify S100A12 and use it to study the antimicrobial affect it exerts upon this medically relevant pathogen. The protocol below outlines an improved technique for S100A12 purification in its biologically active state; capable of binding nutrient metals with high affinity and chelating them away from invading microorganisms. Furthermore, the methods below highlight the utility of this protein as a critical reagent to study the mechanism by which innate antimicrobial molecules restrict the growth of bacterial pathogens.
S100A-family proteins have gained appreciation as an important group of innate immune system molecules which participate in immune signaling as well as host defense27. The most well-studied of these is calprotectin (MRP-8/14, calgranulin A/B, S100A8/A9)28,29,30. Calprotectin is a neutrophil-associated protein which forms a heterodimer of the S100A8 and S100A9 subunits which binds transition metals at the dimer interface31. Calprotectin has been shown to possess two metal binding sites: Site 1 can bind Zn2+, Mn2+, or Fe2+, and Site 2 can bind Zn2+ 31,32. Numerous reports have demonstrated that calprotectin has antimicrobial activities against diverse pathogens including Staphylococcus aureus, Candida albicans, Acinetobacter baumannii, Klebsiella pneumoniae, Escherichia coli, and H. pylori, and that the inhibitory effects are due to the metal chelation activity of calprotectin25,28,29.
Previous work demonstrated calprotectin exerts numerous activities on H. pylori including altering the lipid A structure in the outer membrane, repressing the cag-Type IV secretion system (which is a major proinflammatory virulence factor within H. pylori), inducing biofilm formation, and repressing H. pylori growth and viability in a dose-dependent manner25,33. Furthermore, genetic and biochemical assays revealed the antibacterial activity of calprotectin against H. pylori was largely derived from its ability to bind nutrient zinc25. H. pylori requires zinc, as was determined by previous research which utilized a chemically defined medium to ascertain the micronutrient requirements for this pathogen to grow and proliferate34. Additionally, calprotectin was highly abundant within H. pylori-infected tissues, and associated with neutrophilic infiltrates, indicating the host may be employing calprotectin as an antimicrobial strategy during infection and subsequent inflammation25,35.
Recent evidence from unbiased proteomics screening techniques suggests that under conditions where reactive oxygen species are plentiful, calprotectin undergoes post-translational modifications which alter the hexa-histidine binding site, thereby inhibiting the metal-binding activity of the protein36. As such, we hypothesized that other S100A-family proteins among the wide repertoire of these molecules could potentially act as auxiliary metal-chelators. We selected S100A12 for further study because it was not identified in the aforementioned screen for post-translational modification, it has the capacity to bind zinc, and it is highly abundant in human tissues derived from H. pylori-infected individuals.
Our work indicates that S100A12 can inhibit H. pylori growth and viability in a dose-dependent manner in the G27 strain of H. pylori, and that the antimicrobial activity of this protein can be reversed by the addition of excess nutrient zinc. This work complements our previous work indicating S100A12 exerted antimicrobial activity against PMSS1 and 7.13 strains of H. pylori, demonstrating its broad antibacterial activity against numerous clinical isolates and laboratory-adapted strains of H. pylori18. Together, these results confirm the importance of S100A12 as a mechanism to control bacterial growth and proliferation via nutritional immunity. Future studies of this important host-bacterial interaction could include exploiting the activity of S100A12 to reduce bacterial burden within host tissues, or determining the contribution of this protein to immune signaling in the context of H. pylori infection.

<table><tbody><tr><td>&lt;strong&gt;S100A12 Expression&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>&lt;strong&gt;Expression cells&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>BL 21 (DE3) competent cells</td><td>New England Biolabs</td><td>C25271</td><td></td></tr><tr><td>Autoinduction medium components</td><td></td><td></td><td></td></tr><tr><td>Yeast Extract</td><td>Research Products International</td><td>Y20020-250.0</td><td></td></tr><tr><td>NaCl</td><td>Research Products International</td><td>S23020-500.0</td><td></td></tr><tr><td>Tryptone</td><td>Research Products International</td><td>T60060-250.0</td><td></td></tr><tr><td>FeCl&lt;sub&gt;3&lt;/sub&gt;</td><td>Sigma-Aldrich</td><td>F2877</td><td></td></tr><tr><td>MgSO&lt;sub&gt;4&lt;/sub&gt;</td><td>Research Products International</td><td>M65240-100.0</td><td></td></tr><tr><td>Na&lt;sub&gt;2&lt;/sub&gt;HPO&lt;sub&gt;4&lt;/sub&gt;</td><td>Research Products International</td><td>S23100-500.0</td><td></td></tr><tr><td>KH&lt;sub&gt;2&lt;/sub&gt;PO&lt;sub&gt;4&lt;/sub&gt;</td><td>Research Products International</td><td>P41200-500.0</td><td></td></tr><tr><td>NH&lt;sub&gt;4&lt;/sub&gt;Cl</td><td>Research Products International</td><td>A20424-500.0</td><td></td></tr><tr><td>Na&lt;sub&gt;2&lt;/sub&gt;SO&lt;sub&gt;4&lt;/sub&gt;</td><td>Research Products International</td><td>S25150-500.0</td><td></td></tr><tr><td>Glycerol</td><td>Research Products International</td><td>G22020-1.0</td><td></td></tr><tr><td>D-glucose</td><td>Research Products International</td><td>G32040-500.0</td><td></td></tr><tr><td>lactose</td><td>Sigma-Aldrich</td><td>L2643</td><td></td></tr><tr><td>&lt;strong&gt;Selection agent&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>ampicillin</td><td>Research Products International</td><td>A40040-5.0</td><td></td></tr><tr><td>&lt;strong&gt;S100A12 Purification&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>AKTA Start Chromatography System</td><td>GE</td><td>29-220-94</td><td></td></tr><tr><td>HiTrap Q Sepharaose Fast Flow</td><td>GE</td><td>17-5156-01</td><td></td></tr><tr><td>HiPrep 16/60 S-200 HR</td><td>GE</td><td>17-1166-01</td><td></td></tr><tr><td>Nanodrop lite spectrophotometer</td><td>Thermo Fisher Scientific</td><td>ND-LITE</td><td></td></tr><tr><td>Tris Base</td><td>Research Products International</td><td>T60040-1000.0</td><td></td></tr><tr><td>&lt;em&gt;H. pylori &lt;/em&gt;Culture</td><td></td><td></td><td></td></tr><tr><td>Blood agar plates</td><td>Lab Supply Company</td><td>BBL221261</td><td></td></tr><tr><td>Brucella broth</td><td>Sigma-Aldrich</td><td>B3051</td><td></td></tr><tr><td>Cholesterol (250x)</td><td>Thermo Fisher Scientific</td><td>12531018</td><td></td></tr><tr><td>NaCl</td><td>Sigma-Aldrich</td><td>793566</td><td></td></tr><tr><td>CaCl&lt;sub&gt;2&lt;/sub&gt;</td><td>Sigma-Aldrich</td><td>C4901</td><td></td></tr><tr><td>&amp;beta;-mercaptoethanol</td><td>Sigma-Aldrich</td><td>M6250</td><td></td></tr><tr><td>Tris Base</td><td>Sigma-Aldrich</td><td>T1503</td><td></td></tr><tr><td>Zinc Chloride</td><td>Sigma-Aldrich</td><td>229997</td><td></td></tr></tbody></table>

expression, purification, and antimicrobial activity of s100a12

Calgranulin proteins are important mediators of innate immunity and are members of the S100 class of the EF-hand family of calcium binding proteins. Some S100 proteins have the capacity to bind transition metals with high affinity and effectively sequester them away from invading microbial pathogens in a process that is termed "nutritional immunity". S100A12 (EN-RAGE) binds both zinc and copper and is highly abundant in innate immune cells such as macrophages and neutrophils. We report a refined method for the expression, enrichment and purification of S100A12 in its active, metal-binding configuration. Utilization of this protein in bacterial growth and viability analyses reveals that S100A12 has antimicrobial activity against the bacterial pathogen, Helicobacter pylori. The antimicrobial activity is predicated on the zinc-binding activity of S100A12, which chelates nutrient zinc, thereby starving H. pylori which requires zinc for growth and proliferation.

S100A12 expression and purification
A three-step purification produced ~40 mg of recombinant S100A12 from 50 mL of bacterial culture. The first step was an ammonium sulfate precipitation of endogenous E. coli proteins. This step was followed by anion-exchange chromatography (Figure1A). The protein is tracked by a SDS-PAGE stained with Coomassie Brilliant Blue (Figure 1B). ...

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Expression, Purification, and Antimicrobial Activity of S100A12

Here, we present a method to express and purify S100A12 (calgranulin C). We describe a protocol to measure its antimicrobial activity against the human pathogen H. pylori.

Calgranulin proteins are important mediators of innate immunity and are members of the S100 class of the EF-hand family of calcium binding proteins. Some ...

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8.3K Views.  Fisk University.  Hier presenteren we een methode om S100A12 (Calgranulin C) uit te drukken en te zuiveren. We beschrijven een protocol om zijn antimicrobiële activiteit tegen het menselijke pathogeen H. pylori te meten. 

Video: Expression, Purification, and Antimicrobial Activity of S100A12

Bacterial Expression and Purification of Human Matrix Metalloproteinase-3 using Affinity Chromatography

Matrix metalloproteinases (MMPs) belong to the family of metzincin proteases with central roles in extracellular matrix (ECM) degradation and remodeling, as well as interactions with several growth factors and cytokines. Overexpression of specific MMPs is responsible in several diseases such as cancer, neurodegenerative diseases, and cardiovascular disease. MMPs have been the center of attention recently as targets to develop therapeutics that can treat diseases correlated to MMP overexpression.
To study the MMP mechanism in solution, more facile and robust recombinant protein expression and purification methods are needed for the production of active, soluble MMPs. However, the catalytic domain of most MMPs cannot be expressed in Escherichia coli (E. coli) in soluble form due to lack of posttranslational machinery, whereas mammalian expression systems are usually costly and have lower yields. MMP inclusion bodies must undergo the tedious and laborious process of extensive purification and refolding, significantly reducing the yield of MMPs in native conformation. This paper presents a protocol using Rosetta2(DE3)pLysS (hereafter referred to as R2DP) cells to produce matrix metalloproteinase-3 catalytic domain (MMP-3cd), which contains an N-terminal His-tag followed by pro-domain (Hisx6-pro-MMP-3cd) for use in affinity purification. R2DP cells enhance the expression of eukaryotic proteins through a chloramphenicol-resistant plasmid containing codons normally rare in bacterial expression systems. Compared to the traditional cell line of choice for recombinant protein expression, BL21(DE3), purification using this new strain improved the yield of purified Hisx6-pro-MMP-3cd. Upon activation and desalting, the pro domain is cleaved along with the N-terminal His-tag, providing active MMP-3cd for immediate use in countless in vitro applications. This method does not require expensive equipment or complex fusion proteins and describes rapid production of recombinant human MMPs in bacteria.

His-tag purification, dialysis, and activation are employed to increase yields of soluble, active matrix metalloproteinase-3 catalytic domain protein expression in bacteria. Protein fractions are analyzed via SDS-PAGE gels.

Matrix metalloproteinases (MMPs) belong to the family of metzincin proteases with central roles in extracellular matrix (ECM) degradation and remodeling, ...

A Pipeline to Investigate the Structures and Signaling Pathways of Sphingosine 1-Phosphate Receptors

Lysophospholipids (LPLs) are bioactive lipids that include sphingosine 1-phosphate (S1P), lysophosphatidic acid, etc. S1P, a metabolic product of sphingolipids in the cell membrane, is one of the best-characterized LPLs that regulates a variety of cellular physiological responses via signaling pathways mediated by sphingosine 1-phosphate receptors (S1PRs). This implicated that the S1P-S1PRs signaling system is a remarkable potential therapeutic target for disorders, including multiple sclerosis (MS), autoimmune disorders, cancer, inflammation, and even COVID-19. S1PRs, a small subset of the class A G-protein coupled receptor (GPCR) family, are composed of five subtypes: S1PR1, S1PR2, S1PR3, S1PR4, and S1PR5. The lack of detailed structural information, however, impedes the drug discovery targeting S1PRs. Here, we applied the cryo-electron microscopy method to solve the structure of the S1P-S1PRs complex, and elucidated the mechanism of activation, selective drug recognition, and G-protein coupling by using cell-based functional assays. Other lysophospholipid receptors (LPLRs) and GPCRs can also be studied using this strategy.

S1P exerts its diverse physiological effects through the S1P receptors (S1PRs) subfamily. Here, a pipeline is described to expound on the structures and function of S1PRs.

Lysophospholipids (LPLs) are bioactive lipids that include sphingosine 1-phosphate (S1P), lysophosphatidic acid, etc. S1P, a metabolic product of ...

Implementation of a Permeable Membrane Insert-based Infection System to Study the Effects of Secreted Bacterial Toxins on Mammalian Host Cells

Many bacterial pathogens secrete potent toxins to aid in the destruction of host tissue, to initiate signaling changes in host cells or to manipulate immune system responses during the course of infection. Though methods have been developed to successfully purify and produce many of these important virulence factors, there are still many bacterial toxins whose unique structure or extensive post-translational modifications make them difficult to purify and study in in vitro systems. Furthermore, even when pure toxin can be obtained, there are many challenges associated with studying the specific effects of a toxin under relevant physiological conditions. Most in vitro cell culture models designed to assess the effects of secreted bacterial toxins on host cells involve incubating host cells with a one-time dose of toxin. Such methods poorly approximate what host cells actually experience during an infection, where toxin is continually produced by bacterial cells and allowed to accumulate gradually during the course of infection. This protocol describes the design of a permeable membrane insert-based bacterial infection system to study the effects of Streptolysin S, a potent toxin produced by Group A Streptococcus, on human epithelial keratinocytes. This system more closely mimics the natural physiological environment during an infection than methods where pure toxin or bacterial supernatants are directly applied to host cells. Importantly, this method also eliminates the bias of host responses that are due to direct contact between the bacteria and host cells. This system has been utilized to effectively assess the effects of Streptolysin S (SLS) on host membrane integrity, cellular viability, and cellular signaling responses. This technique can be readily applied to the study of other secreted virulence factors on a variety of mammalian host cell types to investigate the specific role of a secreted bacterial factor during the course of infection.

Here, a method using a permeable membrane insert-based infection system to study the effects of Streptolysin S, a secreted toxin produced by Group A Streptococcus, on keratinocytes is described. This system can be readily applied to the study of other secreted bacterial proteins on various host cell types during infection.

Many bacterial pathogens secrete potent toxins to aid in the destruction of host tissue, to initiate signaling changes in host cells or to manipulate ...

Immunology and Infection

Purifying a Fibrinolytic Enzyme from Sipunculus nudus via Affinity Chromatography

Affinity Purification of a Fibrinolytic Enzyme from Sipunculus nudus

The fibrinolytic enzyme from Sipunculus nudus (sFE) is a novel fibrinolytic agent that can both activate plasminogen into plasmin and degrade fibrin directly, showing great advantages over traditional thrombolytic agents. However, due to the lack of structural information, all the purification programs for sFE are based on multistep chromatography purifications, which are too complicated and costly. Here, an affinity purification protocol of sFE is developed for the first time based on a crystal structure of sFE; it includes preparation of the crude sample and the lysine/arginine-agarose matrix affinity chromatography column, affinity purification, and characterization of the purified sFE. Following this protocol, a batch of sFE can be purified within 1 day. Moreover, the purity and activity of the purified sFE increases to 92% and&#160;19,200 U/mL,&#160;respectively. Thus, this is a simple, inexpensive, and efficient approach for sFE purification. The development of this protocol is of great significance for the further utilization of sFE and other similar agents.

Author Spotlight: Affinity Purification of a Fibrinolytic Enzyme from Sipunculus nudus  

Here, we present an affinity purification method of a fibrinolytic enzyme from Sipunculus nudus that is simple, inexpensive, and efficient.

The fibrinolytic enzyme from Sipunculus nudus (sFE) is a novel fibrinolytic agent that can both activate plasminogen into plasmin and degrade fibrin ...

Antimicrobial Peptides Produced by Selective Pressure Incorporation of Non-canonical Amino Acids

Nature has a variety of possibilities to create new protein functions by modifying the sequence of the individual amino acid building blocks. However, all variations are based on the 20 canonical amino acids (cAAs). As a way to introduce additional physicochemical properties into polypeptides, the incorporation of non-canonical amino acids (ncAAs) is increasingly used in protein engineering. Due to their relatively short length, the modification of ribosomally synthesized and post-translationally modified peptides by ncAAs is particularly attractive. New functionalities and chemical handles can be generated by specific modifications of individual residues. The selective pressure incorporation (SPI) method utilizes auxotrophic host strains that are deprived of an essential amino acid in chemically defined growth media. Several structurally and chemically similar amino acid analogs can then be activated by the corresponding aminoacyl-tRNA synthetase and provide residue-specific cAA(s) &#8594; ncAA(s) substitutions in the target peptide or protein sequence. Although, in the context of the SPI method, ncAAs are also incorporated into the host proteome during the phase of recombinant gene expression, the majority of the cell&#39;s resources are assigned to the expression of the target gene. This enables efficient residue-specific incorporation of ncAAs often accompanied with high amounts of modified target. The presented work describes the in vivo incorporation of six proline analogs into the antimicrobial peptide nisin, a lantibiotic naturally produced by Lactococcus lactis. Antimicrobial properties of nisin can be changed and further expanded during its fermentation and expression in auxotrophic Escherichia coli strains in defined growth media. Thereby, the effects of residue-specific replacement of cAAs with ncAAs can deliver changes in antimicrobial activity and specificity. Antimicrobial activity assays and fluorescence microscopy are used to test the new nisin variants for growth inhibition of a Gram-positive Lactococcus lactis indicator strain. Mass spectroscopy is used to confirm ncAA incorporation in bioactive nisin variants.

The protocol presents the Escherichia coli-based selective pressure incorporation of non-canonical amino acids (ncAAs) into the lactococcal antimicrobial peptide nisin. Its properties can be changed during recombinant expression via substitution with desired ncAAs in defined growth media. Resulting changes in bioactivity are mapped by growth inhibition assays and fluorescence microscopy.

Nature has a variety of possibilities to create new protein functions by modifying the sequence of the individual amino acid building blocks. However, all ...

Bioengineering

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Since most cellular processes are mediated by macromolecular assemblies, the systematic identification of protein-protein interactions (PPI) and the identification of the subunit composition of multi-protein complexes can provide insight into gene function and enhance understanding of biological systems1, 2. Physical interactions can be mapped with high confidence vialarge-scale isolation and characterization of endogenous protein complexes under near-physiological conditions based on affinity purification of chromosomally-tagged proteins in combination with mass spectrometry (APMS). This approach has been successfully applied in evolutionarily diverse organisms, including yeast, flies, worms, mammalian cells, and bacteria1-6. In particular, we have generated a carboxy-terminal Sequential Peptide Affinity (SPA) dual tagging system for affinity-purifying native protein complexes from cultured gram-negative Escherichia coli, using genetically-tractable host laboratory strains that are well-suited for genome-wide investigations of the fundamental biology and conserved processes of prokaryotes1, 2, 7. Our SPA-tagging system is analogous to the tandem affinity purification method developed originally for yeast8, 9, and consists of a calmodulin binding peptide (CBP) followed by the cleavage site for the highly specific tobacco etch virus (TEV) protease and three copies of the FLAG epitope (3X FLAG), allowing for two consecutive rounds of affinity enrichment. After cassette amplification, sequence-specific linear PCR products encoding the SPA-tag and a selectable marker are integrated and expressed in frame as carboxy-terminal fusions in a DY330 background that is induced to transiently express a highly efficient heterologous bacteriophage lambda recombination system10. Subsequent dual-step purification using calmodulin and anti-FLAG affinity beads enables the highly selective and efficient recovery of even low abundance protein complexes from large-scale cultures. Tandem mass spectrometry is then used to identify the stably co-purifying proteins with high sensitivity (low nanogram detection limits).
Here, we describe detailed step-by-step procedures we commonly use for systematic protein tagging, purification and mass spectrometry-based analysis of soluble protein complexes from E. coli, which can be scaled up and potentially tailored to other bacterial species, including certain opportunistic pathogens that are amenable to recombineering. The resulting physical interactions can often reveal interesting unexpected components and connections suggesting novel mechanistic links. Integration of the PPI data with alternate molecular association data such as genetic (gene-gene) interactions and genomic-context (GC) predictions can facilitate elucidation of the global molecular organization of multi-protein complexes within biological pathways. The networks generated for E. coli can be used to gain insight into the functional architecture of orthologous gene products in other microbes for which functional annotations are currently lacking.

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Affinity purification of tagged proteins in combination with mass spectrometry (APMS) is a powerful method for the systematic mapping of protein interaction networks and for investigating the mechanistic basis of biological processes. Here, we describe an optimized sequential peptide affinity (SPA) APMS procedure developed for the bacterium Escherichia coli that can be used to isolate and characterize stable multi-protein complexes to near homogeneity even starting from low copy numbers per cell.

Since most cellular processes are mediated by macromolecular assemblies, the systematic identification of protein-protein interactions (PPI) and the ...

Biology

Purification of Human S100A12 and Its Ion-induced Oligomers for Immune Cell Stimulation

In this protocol, we describe a method to purify human calcium-binding protein S100A12 and its ion-induced oligomers from Escherichia coli culture for immune cell stimulations. This protocol is based on a two-step chromatography strategy, which comprises protein pre-purification on an anion-exchange chromatography column and a subsequent polishing step on a hydrophobic-interaction column. This strategy produces S100A12 protein of high purity and yield at manageable costs. For functional assays on immune cells eventual remnant endotoxin contamination requires careful monitoring and further cleaning steps to obtain endotoxin-free protein. The majority of endotoxin contaminations can be excluded by anion-exchange chromatography. To deplete residual contaminations, this protocol describes a removal step with centrifugal filters. Depending on the available ion-strength S100A12 can arrange into different homomultimers. To investigate the relationship between structure and function, this protocol further describes ion-treatment of S100A12 protein followed by chemical crosslinking to stabilize S100A12 oligomers and their subsequent separation by size-exclusion chromatography. Finally, we describe a cell-based assay that confirms the biological activity of the purified protein and confirms LPS-free preparation.

This protocol describes a purification method for recombinant tag-free calcium binding protein S100A12 and its ion-induced oligomers for human monocyte stimulation assays.

In this protocol, we describe a method to purify human calcium-binding protein S100A12 and its ion-induced oligomers from Escherichia coli culture for ...

Budding Yeast Protein Extraction and Purification for the Study of Function, Interactions, and Post-translational Modifications

Homogenization by bead beating is a fast and efficient way to release DNA, RNA, proteins, and metabolites from budding yeast cells, which are notoriously hard to disrupt. Here we describe the use of a bead mill homogenizer for the extraction of proteins into buffers optimized to maintain the functions, interactions and post-translational modifications of proteins. Logarithmically growing cells expressing the protein of interest are grown in a liquid growth media of choice. The growth media may be supplemented with reagents to induce protein expression from inducible promoters (e.g. galactose), synchronize cell cycle stage (e.g. nocodazole), or inhibit proteasome function (e.g. MG132). Cells are then pelleted and resuspended in a suitable buffer containing protease and/or phosphatase inhibitors and are either processed immediately or frozen in liquid nitrogen for later use. Homogenization is accomplished by six cycles of 20 sec&#160;bead-beating (5.5 m/sec), each followed by one minute incubation on ice. The resulting homogenate is cleared by centrifugation and small particulates can be removed by filtration. The resulting cleared whole cell extract (WCE) is precipitated using 20% TCA for direct analysis of total proteins by SDS-PAGE followed by Western blotting. Extracts are also suitable for affinity purification of specific proteins, the detection of post-translational modifications, or the analysis of co-purifying proteins. As is the case for most protein purification protocols, some enzymes and proteins may require unique conditions or buffer compositions for their purification and others may be unstable or insoluble under the conditions stated. In the latter case, the protocol presented may provide a useful starting point to empirically determine the best bead-beating strategy for protein extraction and purification. We show the extraction and purification of an epitope-tagged SUMO E3 ligase, Siz1, a cell cycle regulated protein that becomes both sumoylated and phosphorylated, as well as a SUMO-targeted ubiquitin ligase subunit, Slx5.

The preparation of high quality yeast cell extracts is a necessary first step in the analysis of individual proteins or entire proteomes. Here we describe a fast, efficient, and reliable homogenization protocol for budding yeast cells that has been optimized to preserve protein functions, interactions, and post-translational modifications.

Homogenization by bead beating is a fast and efficient way to release DNA, RNA, proteins, and metabolites from budding yeast cells, which are notoriously ...

Production and Visualization of Bacterial Spheroplasts and Protoplasts to Characterize Antimicrobial Peptide Localization

The use of confocal microscopy as a method to assess peptide localization patterns within bacteria is commonly inhibited by the resolution limits of conventional light microscopes. As the resolution for a given microscope cannot be easily enhanced, we present protocols to transform the small rod-shaped gram-negative Escherichia coli (E. coli) and gram-positive Bacillus megaterium (B. megaterium) into larger, easily imaged spherical forms called spheroplasts or protoplasts. This transformation allows observers to rapidly and clearly determine whether peptides lodge themselves into the bacterial membrane (i.e., membrane localizing) or cross the membrane to enter the cell (i.e., translocating). With this approach, we also present a systematic method to characterize peptides as membrane localizing or translocating. While this method can be used for a variety of membrane-active peptides and bacterial strains, we demonstrate the utility of this protocol by observing the interaction of Buforin II P11A (BF2 P11A), an antimicrobial peptide (AMP), with E. coli spheroplasts and B. megaterium protoplasts.

Here we present a protocol to produce gram-negative Escherichia coli (E. coli) spheroplasts and gram-positive Bacillus megaterium (B. megaterium) protoplasts to clearly visualize and rapidly characterize peptide-bacteria interactions. This provides a systematic method to define membrane localizing and translocating peptides.

The use of confocal microscopy as a method to assess peptide localization patterns within bacteria is commonly inhibited by the resolution limits of ...

Anion-Exchange Chromatography-Based Protein Purification: A Separation Technique to Isolate a Protein of Interest From Dialyzed Bacterial Lysate Based on Net Charge

Source: Fuehner, S., et al. <a href="https://www.jove.com/v/60065">Purification of Human S100A12 and Its Ion-induced Oligomers for Immune Cell Stimulation</a> J. Vis. Exp. (2019)
In this video, we demonstrate an anion-exchange chromatography technique to purify human calcium-binding protein S100A12 based on the net surface charge of the protein from an Escherichia coli culture.

Source: Fuehner, S., et al. Purification of Human S100A12 and Its Ion-induced Oligomers for Immune Cell Stimulation J. Vis. Exp. (2019)
In this video, we ...

Expression, Purification, and Antimicrobial Activity of S100A12

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