This work has been supported by Elizabeth E. Kennedy Research Award.

1. Preparation of Producer Strain
<ol>
	<li>Streak a pneumococcal strain to be tested for bacteriocin production on a 5% sheep blood tryptic soy agar plate from -80 &#176;C freezer stocks. 
	NOTE: The use of blood plates for initial growth of the strain to be tested for inhibition greatly increases the reproducibility of the assay. Additionally, other non-pneumococcal strains that produce bacteriocins can be used although growth conditions may need to be modified for a specific organism. We have used Streptococcus mitis and Lactococcus lactis in the overlay assay successfully.</li>
	<li>Incubate the plate overnight (O/N) at 37 &#176;C with 5% CO2.</li>
	<li>After incubation of the producer strain, prepare the tryptic soy agar (TSA) plate by pipetting 3,000 to 4,000 units of catalase onto plates containing 25 ml of TSA and spread the catalase solution using sterile glass beads. Let the plate dry for about 10&#160;min&#160;under a biological safety cabinet.</li>
	<li>Collect a visible quantity of bacteria onto a pipette tip. Stab the pipette tip into the dried TSA plate. 
	NOTE: More than one producer strain can be stabbed into a single TSA plate. It is important to space out the stabs so that resulting halos do not overlap.
	<ol>
		<li>If possible, include known bacteriocin producer as a positive control and the strain to be used in the overlay as a negative control. 
		NOTE: Positive and negative controls are have been previously published and are available upon request10.</li>
	</ol>
	</li>
	<li>Incubate TSA plate containing multiple stabs at 37 &#176;C with 5% CO2 for 6 hr.</li>
</ol>
2. Making Glycerol Stocks of the Overlay Strain
<ol>
	<li>Prepare glycerol stocks (cultures grown to mid-exponential phase and then stored at -80 &#176;C after the addition of glycerol) prior to the day of the overlay assay. Inoculate 5-10 colonies of pneumococcal strain to be tested for sensitivity or pheromone secretion in Todd-Hewitt medium with 0.5% yeast extract (THY). 
	NOTE: Construction of BlpC inducible reporters has been previously described2 and strains are available upon request.</li>
	<li>Incubate 5-10 colonies in glass tubes with 5 ml of THY with tightly closed lids in a 37 &#176;C water bath without shaking.</li>
	<li>Incubate cultures at 37 &#176;C until they reach an OD620 of 0.3 to 0.5. 
	NOTE: This will take approximately 4-5 hr depending on the strain used.
	<ol>
		<li>Gently invert the tube a few times prior to measuring the OD.</li>
	</ol>
	</li>
	<li>If the experiment cannot be performed the same day or the strain will be used multiple times in the future, make glycerol stocks and resume the experiment at a later date. For glycerol stocks, add glycerol to cultures to a final concentration of 20%. Aliquot cultures into 1.5 ml microcentrifuge tubes and store at -80 &#176;C. NOTE: Samples can be stored for months at -80 &#176;C. If not making glycerol stocks, use samples directly for overlay assay.</li>
</ol>
3. Overlay Assay
<ol>
	<li>Just prior to overlay application, mix the overlay components. In a 15 ml conical tube, add 5 ml of THY, 3,000-4,000 U of catalase, and 200 &#181;l of the overlay strain broth culture that was either grown that day or a glycerol stock of the culture that was thawed at room temperature. If using the reporter strain, add 50 &#181;l of X-gal (40 mg/ml) to the overlay mixture. Use one conical tube per plate.</li>
	<li>Equilibrate overlay mixture at room temperature prior to addition of molten TSA.</li>
	<li>Remove TSA plate with stabbed strain from incubator. Melt solid TSA in microwave and keep at 55 &#176;C water bath until ready to use. Add 3 ml of molten TSA with 1.5% agar cooled to 55 &#176;C to overlay mixture.
	<ol>
		<li>Prepare the overlay mixture immediately before pipetting, the mixture will begin to solidify very quickly. NOTE: If the overlay begins to solidify before plating, the results will be uninterpretable.</li>
	</ol>
	</li>
	<li>Mix the overlay mixture by pipetting up and down several times with a 5 ml pipet being careful not to introduce bubbles into the mixture. Slowly pipette overlay mixture directly on to the stabbed TSA plate. Keep the plate on the benchtop for few minutes allowing the agar to harden.
	<ol>
		<li>Do not rotate the plate to distribute the overlay mixture, this will pull growth from the stabbed culture into the overlay.</li>
	</ol>
	</li>
	<li>Carefully place TSA plate with overlay into 37 &#176;C incubator containing 5% CO2 O/N (approximately 16-18 hr).</li>
	<li>Observe the plates after overnight growth. The plates should appear opaque from growth of the overlay strain except in areas where inhibition or pheromone signaling has occurred. These will appear as either clear or blue zones around the stabbed strain, respectively. 
	NOTE: Although measurements of the diameter of blue or clearing can be determined for quantitative assessment, differences in the diameter can also vary depending on the amount of bacteria that was stabbed into the plate. The overlay assay is a qualitative assay, any quantitative assessment should be interpreted with caution. Any visible clearing as compared to the negative control is regarded as activity.</li>
</ol>

<ol>
	<li>Dawid, S., Roche, A. M., Weiser, J. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+blp+bacteriocins+of+Streptococcus+pneumoniae+mediate+intraspecies+competition+both+in+vitro+and+in+vivo.">The blp bacteriocins of Streptococcus pneumoniae mediate intraspecies competition both in vitro and in vivo.</a> Infect Immun. 75 (1), 443-451 (2007).</li><li>Sawa, N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+and+characterization+of+enterocin+W,+a+novel+two-peptide+lantibiotic+produced+by+Enterococcus+faecalis+NKR-4-1.">Isolation and characterization of enterocin W, a novel two-peptide lantibiotic produced by Enterococcus faecalis NKR-4-1.</a> Appl Environ Microbiol. 78 (3), 900-903 (2012).</li><li>Kochan, T. J., Dawid, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+HtrA+protease+of+Streptococcus+pneumoniae+controls+density-dependent+stimulation+of+the+bacteriocin+blp+locus+via+disruption+of+pheromone+secretion.">The HtrA protease of Streptococcus pneumoniae controls density-dependent stimulation of the bacteriocin blp locus via disruption of pheromone secretion.</a> J Bacteriol. 195 (7), 1561-1572 (2013).</li><li>Lux, T., Nuhn, M., Hakenbeck, R., Reichmann, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Diversity+of+bacteriocins+and+activity+spectrum+in+Streptococcus+pneumoniae.">Diversity of bacteriocins and activity spectrum in Streptococcus pneumoniae.</a> J Bacteriol. 189 (21), 7741-7751 (2007).</li><li>Reichmann, P., Hakenbeck, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Allelic+variation+in+a+peptide-inducible+two-component+system+of+Streptococcus+pneumoniae.">Allelic variation in a peptide-inducible two-component system of Streptococcus pneumoniae.</a> FEMS Microbiol Lett. 190 (2), 231-236 (2000).</li><li>Saizieu, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microarray-based+identification+of+a+novel+Streptococcus+pneumoniae+regulon+controlled+by+an+autoinduced+peptide.">Microarray-based identification of a novel Streptococcus pneumoniae regulon controlled by an autoinduced peptide.</a> J Bacteriol. 182 (17), 4696-4703 (2000).</li><li>Barbour, A., Philip, K., Muniandy, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enhanced+production,+purification,+characterization+and+mechanism+of+action+of+salivaricin+9+lantibiotic+produced+by+Streptococcus+salivarius+NU10.">Enhanced production, purification, characterization and mechanism of action of salivaricin 9 lantibiotic produced by Streptococcus salivarius NU10.</a> PLoS One. 8 (10), 77751 (2013).</li><li>Wladyka, B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation,+biochemical+characterization,+and+cloning+of+a+bacteriocin+from+the+poultry-associated+Staphylococcus+aureus+strain+CH-91.">Isolation, biochemical characterization, and cloning of a bacteriocin from the poultry-associated Staphylococcus aureus strain CH-91.</a> Appl Microbiol Biotechnol. 97 (16), 7229-7239 (2013).</li><li>Shea, E. F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bactofencin+a,+a+new+type+of+cationic+bacteriocin+with+unusual+immunity.">Bactofencin a, a new type of cationic bacteriocin with unusual immunity.</a> 4 (6), 00498-00413 (2013).</li><li>Son, M. R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Conserved+mutations+in+the+pneumococcal+bacteriocin+transporter+gene,+blpA,+result+in+a+complex+population+consisting+of+producers+and+cheaters.">Conserved mutations in the pneumococcal bacteriocin transporter gene, blpA, result in a complex population consisting of producers and cheaters.</a> MBio. 2 (5), (2011).</li><li>Kochan, T. J., Dawid, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+HtrA+protease+of+Streptococcus+pneumoniae+controls+density-dependent+stimulation+of+the+bacteriocin+blp+locus+via+disruption+of+pheromone+secretion.">The HtrA protease of Streptococcus pneumoniae controls density-dependent stimulation of the bacteriocin blp locus via disruption of pheromone secretion.</a> J Bacteriol. 195, 1561-1572 (2013).</li><li>Widdick, D. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cloning+and+engineering+of+the+cinnamycin+biosynthetic+gene+cluster+from+Streptomyces+cinnamoneus+cinnamoneus+DSM+40005.">Cloning and engineering of the cinnamycin biosynthetic gene cluster from Streptomyces cinnamoneus cinnamoneus DSM 40005.</a> Proc Natl Acad Sci U S A. 100 (7), 4316-4321 (2003).</li><li>Begley, M., Cotter, P. D., Hill, C., Ross, R. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+a+novel+two-peptide+lantibiotic,+lichenicidin,+following+rational+genome+mining+for+LanM+proteins.">Identification of a novel two-peptide lantibiotic, lichenicidin, following rational genome mining for LanM proteins.</a> Appl Environ Microbiol. 75 (17), 5451-5460 (2009).</li></ol>

The authors have nothing to disclose.

This overlay assay is a rapid way to determine the range of activity for bacteriocin producers and to demonstrate competitive interactions that may occur among pneumococcal strains. The overlay assay can be adapted to use for screening multiple strains for bacteriocin production on a single plate. We have successfully screened large strain collections with this assay by using a 48-pin replicator to inoculate SBA plates from one half of a 96-well plate. After overnight incubation, growth is transferred to the TSA plate using the replicator and piercing the agar surface of the plate with the pins of the replicator.
Other bacterially secreted antimicrobial peptides that are regulated in a density dependent manner like lantibiotics can also be examined using the overlay technique7,12,13. This is especially useful when purification of a bacteriocin or lantibiotic is difficult. Though supernatants can be tested for antimicrobial activity, expression of the blp derived bacteriocins in broth is very limited or nonexistent (data not shown). The overlay assay allows for growth to a higher density which is not achieved when organisms are grown in liquid. Growth on a solid medium might also more closely reflect the in vivo growth conditions of the nasopharynx.
The overlay assay can also be used to examine the ability of the stabbed strain to secrete the bacteriocin specific signaling pheromone. This requires construction of a reporter strain which expresses the pheromone receptor protein and in which a pheromone responsive promoter is placed upstream of the lacZ gene. Appreciation of pheromone secretion by a stabbed strain is particularly useful as a readout of blp locus activity if the stabbed strain does not inhibit the overlay strain. The inability to inhibit the overlay strain could be the result of a non-functional blp locus (such as in a strain with a transporter mutation) or because the bacteriocins secreted are not active against the particular overlay strain tested. The reporter strain overlay provides additional information that the locus in the producer has a fully functional two component system and BlpA transporter allowing for upregulation and secretion of the pheromone. This implies that any encoded bacteriocins are also secreted.
There are some limitations to this assay. The overlay assay is a qualitative assay, so comparisons between the inhibitory activity or pheromone secretion of different strains have to be made carefully. Growth rates and conditions should be considered when comparing different strains because the outcome of the assay relies heavily on the growth rate of the overlay and stabbed strains. The addition of catalase to both the plate and the overlay is important in order to remove the inhibitory effects of pneumococcal H2O2 production on the growth of the overlay strain, in particular when using catalase negative organism in the overlay. Given the known diversity of genomic content in the pneumococcal population, any inhibitory activity seen with this assay cannot be automatically attributed to the blp locus without deletional analysis.

Streptococcus pneumoniae, a common colonizer of the polymicrobial community of the nasopharynx, is able to compete with other pneumococci and closely related species through the production of bacterially produced antimicrobial peptides (bacteriocins). Every fully-sequenced pneumococcal strain examined to date contains a version of the bacteriocin-like peptide locus, blp. Bacteriocin production by pneumococcus has been demonstrated to be important in the outcome of both in vitro and in vivo competition1-4. Competitive dynamics are influenced by the expression of diverse bacteriocins along with cognate immunity proteins in response to a specific peptide pheromone. Induction of the blp locus is controlled by a quorum sensing system in which a peptide pheromone, BlpC, binds to the sensor kinase, BlpH, and initiates a signaling cascade resulting in the transcription of the blp locus5,6. There are four allelic variations of BlpC that each bind to its cognate BlpH6. For the cell to survive the effects of its own bacteriocin, the genes that encode cognate immunity proteins are transcribed on the same operon as each of the bacteriocin genes. Killing occurs if a competitor strain is not able to upregulate the blp locus in response to exogenous pheromone or, if the strain lacks the specific immunity gene required for protection. The transporter complex, BlpAB is required for the secretion and processing of the peptide pheromone and the bacteriocin peptides2,4. Recently, it has been shown that a significant proportion of pneumococcal strains are &#8220;cheaters&#8221; meaning they have a conserved mutation in the blpA gene which renders them unable to secrete pheromones and bacteriocins1,2. These strains are able to respond to exogenous BlpC2 secreted by neighboring strains allowing for the production of immunity proteins.
Although, crude preparations of bacteriocins from supernatants can be prepared from producer strains using biochemical methods steps to achieve purity, this approach is not useful for screening large collections of isolates and if the level of bacteriocin expression is low in broth grown cultures2,7-9. The overlay assay is used as a rapid way to investigate the competitive dynamics between strains that may exist in vitro. To do so, a pneumococcal strain is pre-inoculated onto an agar plate and allowed to grow to achieve local bacterial concentrations sufficient for induction of the blp locus. A second strain is then inoculated into a molten soft agar solution which is then applied over the pre-inoculated strain to test for sensitivity. To evaluate for activity of the blp locus (independent of inhibitory activity), strains can be overlaid with a series of three previously described BlpC reporter strains. These strains were constructed to contain one of three different blpH alleles that respond to the three most common BlpC pheromones secreted by the pneumococci. The reporter strains have an integrated lacZ gene that is under the control of a BlpH dependent promoter and carry a deletion in the blpC gene that prevents self-stimulation10,11.

<table><tbody><tr><td>Trypticase Soy Agar with 5% Sheep Blood</td><td>Fisher</td><td>B21261X</td><td>For growth from freezer cultures</td></tr><tr><td>Catalase</td><td>Sigma</td><td>C100-500mg</td><td>4,741 Units per plate</td></tr><tr><td>Todd Hewitt Broth + Yeast Extract (THY)</td><td>Fisher</td><td>DF0492-17-6&amp;nbsp;</td><td>30 g of THB, 5 g yeast extract, 1 L ddH&lt;sub&gt;2&lt;/sub&gt;O autoclave</td></tr><tr><td>Trypticase Soy Broth + Agar plates (TSA)</td><td>Fisher</td><td>B11768&amp;nbsp;</td><td>30 g of TS, 15 g agar, 1 L ddH&lt;sub&gt;2&lt;/sub&gt;O autoclave</td></tr><tr><td>5-bromo-4-chloro-3-indolyl &amp;beta;-D-galactopyranoside (X-gal)</td><td>Sigma</td><td>B4252-50MG</td><td>Dissolve in dimethylformamide</td></tr><tr><td>Petri dishes</td><td>Fisher</td><td>FB0875712</td><td></td></tr><tr><td>Spectrophometer</td><td></td><td></td><td>Measures the OD&lt;sub&gt;620&lt;/sub&gt; of cultures</td></tr><tr><td>37 &amp;deg;C water bath</td><td></td><td></td><td></td></tr><tr><td>37 &amp;deg;C incubator with 5% CO2</td><td></td><td></td><td></td></tr><tr><td>15 ml conical tube</td><td></td><td></td><td></td></tr></tbody></table>

using the overlay assay to qualitatively measure bacterial production of and sensitivity to pneumococcal bacteriocins

Streptococcus pneumoniae colonizes the highly diverse polymicrobial community of the nasopharynx where it must compete with resident organisms. We have shown that bacterially produced antimicrobial peptides (bacteriocins) dictate the outcome of these competitive interactions. All fully-sequenced pneumococcal strains harbor a bacteriocin-like peptide (blp) locus. The blp locus encodes for a range of diverse bacteriocins and all of the highly conserved components needed for their regulation, processing, and secretion. The diversity of the bacteriocins found in the bacteriocin immunity region (BIR) of the locus is a major contributor of pneumococcal competition. Along with the bacteriocins, immunity genes are found in the BIR and are needed to protect the producer cell from the effects of its own bacteriocin. The overlay assay is a quick method for examining a large number of strains for competitive interactions mediated by bacteriocins. The overlay assay also allows for the characterization of bacteriocin-specific immunity, and detection of secreted quorum sensing peptides. The assay is performed by pre-inoculating an agar plate with a strain to be tested for bacteriocin production followed by application of a soft agar overlay containing a strain to be tested for bacteriocin sensitivity. A zone of clearance surrounding the stab indicates that the overlay strain is sensitive to the bacteriocins produced by the pre-inoculated strain. If no zone of clearance is observed, either the overlay strain is immune to the bacteriocins being produced or the pre-inoculated strain does not produce bacteriocins. To determine if the blp locus is functional in a given strain, the overlay assay can be adapted to evaluate for peptide pheromone secretion by the pre-inoculated strain. In this case, a series of four lacZ-reporter strains with different pheromone specificity are used in the overlay.

There are two possible outcomes in the overlay assay. It should be possible to see growth of the stabbed strain after overnight incubation. In Figure 1A, the overlay strain is sensitive to the bacteriocins being produced. A zone of clearance can be visualized surrounding the stabbed strain. Additionally, swirling of the stabbed strain into the overlay mixture is possible and can be seen in the Figure 1A. In Figure 1B, the overlay strain is immune to the bacteriocins being secreted as noted by an absence of a halo surrounding the stab. It is also possible that the stabbed strain is not secreting bacteriocins. For the signaling assay, two different outcomes are possible. The stabbed strain is able to secrete pheromone that interacts with the histidine kinase of the overlay strain, as seen through the breakdown of X-gal as shown in Figure 2A. If the pheromone does not activate transcription of the blp locus in the reporter strain, or if the stabbed strain does not secrete pheromone, breakdown of X-gal will not occur as shown in Figure 2B.
<img alt="Figure 1" fo:content-width="5in" src="/files/ftp_upload/51876/51876fig1highres.jpg" width="500" /> 
Figure 1. Appearance of blp mediated inhibition and immunity in an overlay assay. (A) Strain P133, a bacteriocin producer was spiked into a TSA plate and allowed to grow for 6 hr. Strain P250, a bacteriocin negative strain, was inoculated into the overlay. Plates were photographed after O/N incubation. A zone of clearance is indicated by the arrow. (B) Strain P133 was spiked into a TSA plate and incubated for 6 hr. Strain 130, containing a frameshift mutation in blpA, was inoculated into the overlay. After O/N incubation, plates were photographed.
<img alt="Figure 2" fo:content-width="5in" src="/files/ftp_upload/51876/51876fig2highres.jpg" width="500" /> 
Figure 2. Pheromone mediated activation of blp locus in signaling assay. (A) Strain P133, a BlpC type R6 secretor, was spiked into a TSA plate and incubated for 6 hr. Strain P981, a BlpC type R6 reporter with a deletion in BlpC, was inoculated into the overlay. Photographs were taken after O/N incubation. (B) P133 was spiked into a TSA plate. After incubation for 6 hr, P845, a BlpC type P164 reporter with a deletion in BlpC, was inoculated into the overlay. Photographs were taken after O/N growth.

Watch this Scientific Journal Video about Using the Overlay Assay to Qualitatively Measure Bacterial Production of and Sensitivity to Pneumococcal Bacteriocins at JoVE.com

Using the Overlay Assay to Qualitatively Measure Bacterial Production of and Sensitivity to Pneumococcal Bacteriocins

Competition in Streptococcus pneumoniae is mediated by bacteriocins, small antimicrobial peptides with inhibitory activity towards pneumococcus and other related species.&#160; Here we describe an optimized bacterial overlay assay that allows for the characterization of bacteriocin activity and inhibitory spectrum, bacteriocin-specific immunity, and detection of secreted quorum sensing peptides.

Streptococcus pneumoniae colonizes the highly diverse polymicrobial community of the nasopharynx where it must compete with resident organisms.  We have ...

using-overlay-assay-to-qualitatively-measure-bacterial-production

Universidad San Sebastian

Research

JoVE Journal

Immunology and Infection

13.4K Views.  University of Michigan. Competition in Streptococcus pneumoniae is mediated by bacteriocins, small antimicrobial peptides with inhibitory activity towards pneumococcus and other related species.  Here we describe an optimized bacterial overlay assay that allows for the characterization of bacteriocin activity and inhibitory spectrum, bacteriocin-specific immunity, and detection of secreted quorum sensing peptides. 

Video: Using the Overlay Assay to Qualitatively Measure Bacterial Production of and Sensitivity to Pneumococcal Bacteriocins

An Assay for Quantifying Protein-RNA Binding in Bacteria

In the initiation step of protein translation, the ribosome binds to the initiation region of the mRNA. Translation initiation can be blocked by binding of an RNA binding protein (RBP) to the initiation region of the mRNA, which interferes with ribosome binding. In the presented method, we utilize this blocking phenomenon to quantify the binding affinity of RBPs to their cognate and non-cognate binding sites. To do this, we insert a test binding site in the initiation region of a reporter mRNA and induce the expression of the test RBP. In the case of RBP-RNA binding, we observed a sigmoidal repression of the reporter expression as a function of RBP concentration. In the case of no-affinity or very low affinity between binding site and RBP, no significant repression was observed. The method is carried out in live bacterial cells, and does not require expensive or sophisticated machinery. It is useful for quantifying and comparing between the binding affinities of different RBPs that are functional in bacteria to a set of designed binding sites. This method may be inappropriate for binding sites with high structural complexity. This is due to the possibility of repression of ribosomal initiation by complex mRNA structure in the absence of RBP, which would result in lower basal reporter gene expression, and thus less-observable reporter repression upon RBP binding.

In this method, we quantify the binding affinity of RNA binding proteins (RBPs) to cognate and non-cognate binding sites using a simple, live, reporter assay in bacterial cells. The assay is based on repression of a reporter gene.

In the initiation step of protein translation, the ribosome binds to the initiation region of the mRNA. Translation initiation can be blocked by binding ...

Genetics

A Visual Assay to Monitor T6SS-mediated Bacterial Competition

Type VI secretion systems (T6SSs) are molecular nanomachines allowing Gram-negative bacteria to transport and inject proteins into a wide variety of target cells1,2. The T6SS is composed of 13 core components and displays structural similarities with the tail-tube of bacteriophages3. The phage uses a tube and a puncturing device to penetrate the cell envelope of target bacteria and inject DNA. It is proposed that the T6SS is an inverted bacteriophage device creating a specific path in the bacterial cell envelope to drive effectors and toxins to the surface. The process could be taken further and the T6SS device could perforate other cells with which the bacterium is in contact, thus injecting the effectors into these targets. The tail tube and puncturing device parts of the T6SS are made with Hcp and VgrG proteins, respectively4,5.
The versatility of the T6SS has been demonstrated through studies using various bacterial pathogens. The Vibrio cholerae T6SS can remodel the cytoskeleton of eukaryotic host cells by injecting an "evolved" VgrG carrying a C-terminal actin cross-linking domain6,7. Another striking example was recently documented using Pseudomonas aeruginosa which is able to target and kill bacteria in a T6SS-dependent manner, therefore promoting the establishment of bacteria in specific microbial niches and competitive environment8,9,10.
In the latter case, three T6SS-secreted proteins, namely Tse1, Tse2 and Tse3 have been identified as the toxins injected in the target bacteria (Figure 1). The donor cell is protected from the deleterious effect of these effectors via an anti-toxin mechanism, mediated by the Tsi1, Tsi2 and Tsi3 immunity proteins8,9,10. This antimicrobial activity can be monitored when T6SS-proficient bacteria are co-cultivated on solid surfaces in competition with other bacterial species or with T6SS-inactive bacteria of the same species8,11,12,13.
The data available emphasized a numerical approach to the bacterial competition assay, including time-consuming CFU counting that depends greatly on antibiotic makers. In the case of antibiotic resistant strains like P. aeruginosa, these methods can be inappropriate. Moreover, with the identification of about 200 different T6SS loci in more than 100 bacterial genomes14, a convenient screening tool is highly desirable. We developed an assay that is easy to use and requires standard laboratory material and reagents. The method offers a rapid and qualitative technique to monitor the T6SS-dependent bactericidal/bacteriostasis activity by using a reporter strain as a prey (in this case Escherichia coli DH5&alpha;) allowing a-complementation of the lacZ gene. Overall, this method is graphic and allows rapid identification of T6SS-related phenotypes on agar plates. This experimental protocol may be adapted to other strains or bacterial species taking into account specific conditions such as growth media, temperature or time of contact.

We describe a qualitative assay to monitor bacterial competition mediated by the Pseudomonas aeruginosa type VI secretion system (T6SS). The assay relies on the survival/killing of Escherichia coli target cells carrying a lacZ-reporter. This technique is adjustable to assess the bactericidal/bacteriostasis activity of T6SS-proficient microorganisms.

Type VI secretion systems (T6SSs) are molecular  nanomachines allowing Gram-negative bacteria to transport and inject proteins  into a wide variety of ...

Single Cell Measurements of Vacuolar Rupture Caused by Intracellular Pathogens

Shigella flexneri are pathogenic bacteria that invade host cells entering into an endocytic vacuole. Subsequently, the rupture of this membrane-enclosed compartment allows bacteria to move within the cytosol, proliferate and further invade neighboring cells. Mycobacterium tuberculosis is phagocytosed by immune cells, and has recently been shown to rupture phagosomal membrane in macrophages. We developed a robust assay for tracking phagosomal membrane disruption after host cell entry of Shigella flexneri or Mycobacterium tuberculosis. The approach makes use of CCF4, a FRET reporter sensitive to &beta;-lactamase that equilibrates in the cytosol of host cells. Upon invasion of host cells by bacterial pathogens, the probe remains intact as long as the bacteria reside in membrane-enclosed compartments. After disruption of the vacuole, &beta;-lactamase activity on the surface of the intracellular pathogen cleaves CCF4 instantly leading to a loss of FRET signal and switching its emission spectrum. This robust ratiometric assay yields accurate information about the timing of vacuolar rupture induced by the invading bacteria, and it can be coupled to automated microscopy and image processing by specialized algorithms for the detection of the emission signals of the FRET donor and acceptor. Further, it allows investigating the dynamics of vacuolar disruption elicited by intracellular bacteria in real time in single cells. Finally, it is perfectly suited for high-throughput analysis with a spatio-temporal resolution exceeding previous methods. Here, we provide the experimental details of exemplary protocols for the CCF4 vacuolar rupture assay on HeLa cells and THP-1 macrophages for time-lapse experiments or end points experiments using Shigella flexneri as well as multiple mycobacterial strains such as Mycobacterium marinum, Mycobacterium bovis, and Mycobacterium tuberculosis.

We describe a method for tracking the endomembrane rupture elicited by the intracellular bacteria Shigella flexneri and Mycobacterium tuberculosis upon host cell invasion. Our assay makes use of CCF4, a host cytoplasmic FRET probe in live or fixed cells. This reporter is degraded by an enzyme activity present on the bacterial surface.

Shigella flexneri are pathogenic bacteria that invade host cells entering into an endocytic vacuole. Subsequently, the rupture of this membrane-enclosed ...

Monitoring Changes in Membrane Polarity, Membrane Integrity, and Intracellular Ion Concentrations in Streptococcus pneumoniae Using Fluorescent Dyes

Membrane depolarization and ion fluxes are events that have been studied extensively in biological systems due to their ability to profoundly impact cellular functions, including energetics and signal transductions. While both fluorescent and electrophysiological methods, including electrode usage and patch-clamping, have been well developed for measuring these events in eukaryotic cells, methodology for measuring similar events in microorganisms have proven more challenging to develop given their small size in combination with the more complex outer surface of bacteria shielding the membrane. During our studies of death-initiation in Streptococcus pneumoniae (pneumococcus), we wanted to elucidate the role of membrane events, including changes in polarity, integrity, and intracellular ion concentrations. Searching the literature, we found that very few studies exist. Other investigators had monitored radioisotope uptake or equilibrium to measure ion fluxes and membrane potential and a limited number of studies, mostly in Gram-negative organisms, had seen some success using carbocyanine or oxonol fluorescent dyes to measure membrane potential, or loading bacteria with cell-permeant acetoxymethyl (AM) ester versions of ion-sensitive fluorescent indicator dyes. We therefore established and optimized protocols for measuring membrane potential, rupture, and ion-transport in the Gram-positive organism S. pneumoniae. We developed protocols using the bis-oxonol dye DiBAC4(3) and the cell-impermeant dye propidium iodide to measure membrane depolarization and rupture, respectively, as well as methods to optimally load the pneumococci with the AM esters of the ratiometric dyes Fura-2, PBFI, and BCECF to detect changes in intracellular concentrations of Ca2+, K+, and H+, respectively, using a fluorescence-detection plate reader. These protocols are the first of their kind for the pneumococcus and the majority of these dyes have not been used in any other bacterial species. Though our protocols have been optimized for S. pneumoniae, we believe these approaches should form an excellent starting-point for similar studies in other bacterial species.

Monitoring Changes in Membrane Polarity, Membrane Integrity, and Intracellular Ion Concentrations in Streptococcus pneumoniae Using Fluorescent Dyes

Unlike that seen for eukaryotes, there is a paucity of studies that detail membrane depolarization and ion concentration changes in bacteria, primarily as their small size makes conventional methods of measurement difficult. Here, we detail protocols for monitoring such events in the significant Gram-positive pathogen Streptococcus pneumoniae utilizing fluorescence techniques.

Membrane depolarization and ion fluxes are events that have been studied extensively in biological systems due to their ability to profoundly impact ...

Investigating the Effects of Probiotics on Pneumococcal Colonization Using an In Vitro Adherence Assay

Adherence of Streptococcus pneumoniae (the pneumococcus) to the epithelial lining of the nasopharynx can result in colonization and is considered a prerequisite for pneumococcal infections such as pneumonia and otitis media. In vitro adherence assays can be used to study the attachment of pneumococci to epithelial cell monolayers and to investigate potential interventions, such as the use of probiotics, to inhibit pneumococcal&#160;colonization.&#160;The protocol described here is used to investigate the effects of the probiotic Streptococcus salivarius on the adherence of pneumococci to the human epithelial cell line CCL-23 (sometimes referred to as HEp-2 cells). The assay involves three main steps: 1) preparation of epithelial and bacterial cells, 2) addition of bacteria to epithelial cell monolayers, and 3) detection of adherent pneumococci by viable counts (serial dilution and plating) or quantitative real-time PCR (qPCR). This technique is relatively straightforward and does not require specialized equipment other than a tissue culture setup. The assay can be used to test other probiotic species and/or potential inhibitors of pneumococcal colonization and can be easily modified to address other scientific questions regarding pneumococcal adherence and invasion.

Investigating the Effects of Probiotics on Pneumococcal Colonization Using an In Vitro Adherence Assay

In vitro adherence assays can be used to study the attachment of Streptococcus pneumoniae to epithelial cell monolayers and to investigate potential interventions such as the use of probiotics for inhibiting pneumococcal colonization.

Adherence of Streptococcus pneumoniae (the pneumococcus) to the epithelial lining of the nasopharynx can result in colonization and is considered a ...

Biomimetic Materials to Characterize Bacteria-host Interactions

Bacterial attachment to host cells is one of the earliest events during bacterial colonization of host tissues and thus a key step during infection. The biochemical and functional characterization of adhesins mediating these initial bacteria-host interactions is often compromised by the presence of other bacterial factors, such as cell wall components or secreted molecules, which interfere with the analysis. This protocol describes the production and use of biomimetic materials, consisting of pure recombinant adhesins chemically coupled to commercially available, functionalized polystyrene beads, which have been used successfully to dissect the biochemical and functional interactions between individual bacterial adhesins and host cell receptors. Protocols for different coupling chemistries, allowing directional immobilization of recombinant adhesins on polymer scaffolds, and for assessment of the coupling efficiency of the resulting &#8220;bacteriomimetic&#8221; materials are also discussed. We further describe how these materials can be used as a tool to inhibit pathogen mediated cytotoxicity and discuss scope, limitations and further applications of this approach in studying bacterial - host interactions.

Bacterial attachment to host cells is a key step during host colonization and infection. This protocol describes the generation of polymer-coupled recombinant adhesins as biomimetic materials which allow analysis of the contribution of individual adhesins to these processes, independent of other bacterial factors.

Bacterial attachment to host cells is one of the earliest events during bacterial colonization of host tissues and thus a key step during infection. The ...

Qualitative and Quantitative Assays for Detection and Characterization of Protein Antimicrobials

Initial evaluations of large microbial libraries for potential producers of novel antimicrobial proteins require both qualitative and quantitative methods to screen for target enzymes prior to investing greater research effort and resources. The goal of this protocol is to demonstrate two complementary assays for conducting these initial evaluations. The microslide diffusion assay provides an initial or simple detection screen to enable the qualitative and rapid assessment of proteolytic activity against an array of both viable and heat-killed bacterial target substrates. As a counterpart, the increased sensitivity and reproducibility of the dye-release assay provides a quantitative platform for evaluating and comparing environmental influences affecting the hydrolytic activity of protein antimicrobials. The ability to label specific heat-killed cell culture substrates with Remazol brilliant blue R dye expands this capability to tailor the dye-release assay to characterize enzymatic activity of interest.

Here, we present protocols to rapidly screen and characterize enzymes for antimicrobial activity. The microslide diffusion assay and the dye-release assay utilize target bacterial substrates for qualitative and quantitative enzymatic activity evaluation.

Initial evaluations of large microbial libraries for potential producers of novel antimicrobial proteins require both qualitative and quantitative methods ...

Use of the Soft-agar Overlay Technique to Screen for Bacterially Produced Inhibitory Compounds

The soft-agar overlay technique was originally developed over 70 years ago and has been widely used in several areas of microbiological research, including work with bacteriophages and bacteriocins, proteinaceous antibacterial agents. This approach is relatively inexpensive, with minimal resource requirements. This technique consists of spotting supernatant from a donor strain (potentially harboring a toxic compound(s)) onto a solidified soft agar overlay that is seeded with a bacterial test strain (potentially sensitive to the toxic compound(s)). We utilized this technique to screen a library of Pseudomonas syringae strains for intraspecific killing. By combining this approach with a precipitation step and targeted gene deletions, multiple toxic compounds produced by the same strain can be differentiated. The two antagonistic agents commonly recovered using this technique are bacteriophages and bacteriocins. These two agents can be differentiated using two simple additional tests. Performing a serial dilution on a supernatant containing bacteriophage will result in individual plaques becoming less in number with greater dilution, whereas serial dilution of a supernatant containing bacteriocin will result a clearing zone that becomes uniformly more turbid with greater dilution. Additionally, a bacteriophage will produce a clearing zone when spotted onto a fresh soft agar overlay seeded with the same strain, whereas a bacteriocin will not produce a clearing zone when transferred to a fresh soft agar lawn, owing to the dilution of the bacteriocin.

We describe a simple method for screening bacterial cultures for the production of compounds inhibitory towards other bacteria.

The soft-agar overlay technique was originally developed over 70 years ago and has been widely used in several areas of microbiological research, ...

A High-throughput Shigella-specific Bactericidal Assay

Serum bactericidal assays (SBAs) measure the functional activity of antibodies and have been used for many decades. SBAs directly measure antibody killing activity by assessing the ability of antibodies in serum to bind to bacteria and activate complement. This complement activation results in the lysis and killing of the target bacteria. These assays are valuable because they go beyond quantifying antibody production to elucidate the biological functions that these antibodies have, allowing researchers to study the role that antibodies may play in preventing infection. SBAs have been used to study immune responses for many human pathogens, but there is no widely accepted methodology for Shigella at present. Historically, SBAs have been very labor-intensive, requiring many time-consuming steps to accurately quantify surviving bacteria. This protocol describes a simple, robust, and high-throughput assay that measures functional antibodies specific for Shigella in serum in vitro. The method described here offers many advantages over traditional SBAs, including the use of frozen bacterial stocks, 96 well assay plates, a micro-culture system, and automated colony-counting. All of these modifications make this assay less labor-intensive and more high-throughput. This protocol is simpler and faster to perform than traditional SBAs while still using simple technologies and readily available reagents. The protocol has been successfully applied in multiple independent laboratories and the assay is robust and reproducible. The assay can be used to assess immune responses in pre-clinical as well as clinical studies. Quantifying shigellacidal antibody titers both before and after antigen exposure (either by immunization or infection) allows for a broader understanding of how functional antibody responses are generated and their contribution to protective immunity. The development of this standardized, well-characterized assay may greatly facilitate Shigella vaccine design.

A High-throughput Shigella-specific Bactericidal Assay

Here we present a protocol to measure Shigellacidal activity of antibodies in serum. Serum is mixed with bacteria and exogenous complement, incubated, and the reaction mixture is plated on agar plates. Viable bacteria form colonies which are counted, using an automated colony enumerator, and used to determine the bactericidal titer.

Serum bactericidal assays (SBAs) measure the functional activity of antibodies and have been used for many decades. SBAs directly measure antibody killing ...

Deferred Growth Inhibition Assay to Quantify the Effect of Bacteria-derived Antimicrobials on Competition

Competitive exclusion can occur in microbial communities when, for example, an inhibitor-producing strain outcompetes its competitor for an essential nutrient or produces antimicrobial compounds that its competitor is not resistant to. Here we describe a deferred growth inhibition assay, a method for assessing the ability of one bacterium to inhibit the growth of another through the production of antimicrobial compounds or through competition for nutrients. This technique has been used to investigate the correlation of nasal isolates with the exclusion of particular species from a community. This technique can also be used to screen for lantibiotic producers or potentially novel antimicrobials. The assay is performed by first culturing the test inhibitor-producing strain overnight on an agar plate, then spraying over the test competitor strain and incubating again. After incubation, the extent of inhibition can be measured quantitatively, through the size of the zone of clearing around the inhibitor-producing strain, and qualitatively, by assessing the clarity of the inhibition zone. Here we present the protocol for the deferred inhibition assay, describe ways to minimize variation between experiments, and define a clarity scale that can be used to qualitatively assess the degree of inhibition.

The deferred growth inhibition assay can be used to assess the competition effect by one bacterial isolate on another. Inhibition is quantified by measuring the zone of clearing around the inhibitor-producing isolate, or qualitatively assessed by determining the visible extent of inhibition.

Competitive exclusion can occur in microbial communities when, for example, an inhibitor-producing strain outcompetes its competitor for an essential ...

Using the Overlay Assay to Qualitatively Measure Bacterial Production of and Sensitivity to Pneumococcal Bacteriocins

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Chapters in this video

An Assay for Quantifying Protein-RNA Binding in Bacteria

A Visual Assay to Monitor T6SS-mediated Bacterial Competition

Single Cell Measurements of Vacuolar Rupture Caused by Intracellular Pathogens

Monitoring Changes in Membrane Polarity, Membrane Integrity, and Intracellular Ion Concentrations in Streptococcus pneumoniae Using Fluorescent Dyes

Investigating the Effects of Probiotics on Pneumococcal Colonization Using an In Vitro Adherence Assay

Biomimetic Materials to Characterize Bacteria-host Interactions

Qualitative and Quantitative Assays for Detection and Characterization of Protein Antimicrobials

Use of the Soft-agar Overlay Technique to Screen for Bacterially Produced Inhibitory Compounds

A High-throughput Shigella-specific Bactericidal Assay

Deferred Growth Inhibition Assay to Quantify the Effect of Bacteria-derived Antimicrobials on Competition