Financial support for this research was provided by startup funds from the University of California.

1. Preparation of bacterial cultures
<ol>
	<li>Grow E. coli strain MG1655 with plasmid transposon constructs (previously described in Kim et al.8) overnight in LB with the appropriate antibiotics (25 &#181;g/mL of kanamycin, see Table of Materials) at 37 &#176;C. 
	NOTE: The sequences of the constructs used and the related sequences are available as GenBank20 accession numbers OP581959, OP581957, OP581958, OP717084, and OP717085.</li>
	<li>To achieve steady-state exponential growth, dilute cultures &#8805;100 fold into the M63 medium (100 mM KH2PO4, 1 mM MgSO4, 1.8 &#181;M FeSO4, 15 mM [NH4]2SO4, 0.5 &#181;g/mL thiamine [vitamin B1]) supplemented with a carbon source (0.5% w/v glucose here) and appropriate antibiotics (see Table of Materials).</li>
	<li>Grow cultures at 37 &#176;C until the optical density at 600 nm (OD600) reaches ~0.2. The cultures are ready for use.</li>
</ol>
2. Slide preparation
<ol>
	<li>Prepare a slide by boiling M63 with 0.5% w/v glucose and 1.5% w/v agarose in the microwave to melt the agarose and ensure that it is completely molten and well mixed.</li>
	<li>Allow the mixture to cool to ~55 &#176;C before adding antibiotics and inducers (25 &#181;g/mL Kanamycin and 10 ng/&#181;L anhydrotetracycline [aTc], see Table of Materials).</li>
	<li>Place a microscope slide on the workbench. Stack two more slides perpendicular to the first and place another on top, parallel to the bottom slide. Ensure that there is a gap equal to one slide thickness between the bottom and top slides. Pipette ~1 mL of the M63 agarose mixture into this gap between the slides slowly to create a small gel square.</li>
	<li>Once the gel has solidified (~10-15 min), slide the top slide to remove it. Trim the agarose pad with a razor blade or knife. Then pipette 2.5 &#181;L of the culture (step 1.3) and put the coverslip on top.</li>
	<li>Seal the space between the slide and the coverslip with epoxy (see Table of Materials). Allow the epoxy to dry and the cells to settle onto the agarose pad for at least 1 h at 37 &#176;C.</li>
</ol>
3. Timelapse fluorescence microscopy
<ol>
	<li>Place the prepared sample (step 1.3) on a fluorescence microscope (see Table of Materials) in an environment heated and maintained at 37 &#176;C.
	<ol>
		<li>Set the exposure times appropriate for the camera used for image acquisition. Adjust the illumination intensity to minimize photobleaching. 
		NOTE: An exposure time of 2 s for each wavelength was used for the present study.</li>
		<li>For each wavelength, find a Field of View (FOV) containing minimal fluorescence. Acquire images to use during the analysis for background subtraction.</li>
	</ol>
	</li>
	<li>Set up a protocol to acquire images in a grid at different wavelengths and at regular time intervals.
	<ol>
		<li>Encode timelapse photography into the protocol. Set the acquisition frequency to the desired time interval (20 min here) and the total timelapse duration to the desired length (24 h).</li>
		<li>Encode appropriate wavelengths into the protocol (depending upon the construct used). 
		NOTE: The mCherry excitation peak is at 587 nm and the emission peak at 610 nm21; mVenus is at 515 nm and 527 nm12, while mCerulean3 is at 433 nm and 475 nm11.</li>
		<li>Set the grid size to capture between the desired number of FOVs. 
		&#8203;NOTE: The representative data shown here used 8 x 8 FOVs.</li>
	</ol>
	</li>
</ol>
4. Image analysis
<ol>
	<li>Perform background subtraction on each color channel by using the respective background images acquired in step 3.1.2. For all the analysis steps, we use standard modules in the open-source platform Fiji22 (see Table of Materials).</li>
	<li>Approximate the total population at each point in time by thresholding the mCerulean channel and dividing the threshold area by the average cell area.</li>
	<li>To count the unique excision events, take the time derivative of the mCerulean3 channel. Perform this by subtracting successive images in the mCerulean3 channel. The excision events will be detected in the time derivative as a bright flash of fluorescence.
	<ol>
		<li>Threshold the stack of excision events to eliminate unwanted fluorescence. Note that this process will threshold out parts of the excisions themselves. To fix this, dilate the images to restore the excisions to their original sizes. 
		NOTE: Analyses using similar thresholding and image analysis techniques can be performed on the other fluorescence channels too (e.g., correlate excision events with levels of transposase TnpA [yellow Venus fluorescence] and TnpB [red mCherry fluorescence].</li>
	</ol>
	</li>
</ol>

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C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transposable+elements+as+mutator+genes+in+evolution.">Transposable elements as mutator genes in evolution.</a> Nature. 303 (5918), 633-635 (1983).</li><li>Coufal, N. G., 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=L1+retrotransposition+in+human+neural+progenitor+cells.">L1 retrotransposition in human neural progenitor cells.</a> Nature. 460 (7259), 1127-1131 (2009).</li><li>Kano, H., 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=L1+retrotransposition+occurs+mainly+in+embryogenesis+and+creates+somatic+mosaicism.">L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism.</a> Genes &amp; Development. 23 (11), 1303-1312 (2009).</li><li>Belancio, V. P., Deininger, P. L., Roy-Engel, A. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=LINE+dancing+in+the+human+genome:+transposable+elements+and+disease.">LINE dancing in the human genome: transposable elements and disease.</a> Genome Medicine. 1 (10), 97 (2009).</li><li>Goodier, J. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Retrotransposition+in+tumors+and+brains.">Retrotransposition in tumors and brains.</a> Mobile DNA. 5, 11 (2014).</li><li>Kim, N. H., 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=Real-time+transposable+element+activity+in+individual+live+cells.">Real-time transposable element activity in individual live cells.</a> Proceedings of the National Academy of Sciences of the United States of America. 113 (26), 7278-7283 (2016).</li><li>Lutz, R., Bujard, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Independent+and+tight+regulation+of+transcriptional+units+in+Escherichia+coli+via+the+LacR/O,+the+TetR/O+and+AraC/I1-I2+regulatory+elements.">Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements.</a> Nucleic Acids Research. 25 (6), 1203-1210 (1997).</li><li>Calos, M. P., Miller, J. 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L., 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=An+improved+cerulean+fluorescent+protein+with+enhanced+brightness+and+reduced+reversible+photoswitching.">An improved cerulean fluorescent protein with enhanced brightness and reduced reversible photoswitching.</a> PLoS One. 6 (3), 17896 (2011).</li><li>Nagai, T., 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=A+variant+of+yellow+fluorescent+protein+with+fast+and+efficient+maturation+for+cell-biological+applications.">A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications.</a> Nature Biotechnology. 20 (1), 87-90 (2002).</li><li>Kersulyte, D., 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=Transposable+element+ISHp608+of+Helicobacter+pylori:+nonrandom+geographic+distribution,+functional+organization,+and+insertion+specificity.">Transposable element ISHp608 of Helicobacter pylori: nonrandom geographic distribution, functional organization, and insertion specificity.</a> Journal of Bacteriology. 184 (4), 992-1002 (2002).</li><li>Shmakov, S., 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=Diversity+and+evolution+of+class+2+CRISPR-Cas+systems.">Diversity and evolution of class 2 CRISPR-Cas systems.</a> Nature Reviews Microbiology. 15 (3), 169-182 (2017).</li><li>Bao, W., Jurka, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Homologues+of+bacterial+TnpB_IS605+are+widespread+in+diverse+eukaryotic+transposable+elements.">Homologues of bacterial TnpB_IS605 are widespread in diverse eukaryotic transposable elements.</a> Mobile DNA. 4 (1), 12 (2013).</li><li>Siguier, P., Gourbeyre, E., Chandler, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bacterial+insertion+sequences:+their+genomic+impact+and+diversity.">Bacterial insertion sequences: their genomic impact and diversity.</a> FEMS Microbiology Reviews. 38 (5), 865-891 (2014).</li><li>Altae-Tran, H., 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=The+widespread+IS200/IS605+transposon+family+encodes+diverse+programmable+RNA-guided+endonucleases.">The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases.</a> Science. 374 (6563), 57-65 (2021).</li><li>Karvelis, T., 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=Transposon-associated+TnpB+is+a+programmable+RNA-guided+DNA+endonuclease.">Transposon-associated TnpB is a programmable RNA-guided DNA endonuclease.</a> Nature. 599 (7886), 692-696 (2021).</li><li>Kaur, D., Kuhlman, T. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=IS200/IS605+family-associated+TnpB+increases+transposon+activity+and+retention.">IS200/IS605 family-associated TnpB increases transposon activity and retention.</a> bioRxiv. , (2022).</li><li>Benson, 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=GenBank.">GenBank.</a> Nucleic Acids Research. 41, 36-42 (2013).</li><li>Shaner, N. 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The authors declare no conflicts of interest.

The unique method presented here for real-time imaging of transposable element activity in live cells is a sensitive assay that can directly detect transposition in live cells and in real-time and correlate this activity with the expression of accessory proteins. While the throughput is lower than can be accomplished by bulk methods, this method achieves detailed measurements of TE activity and protein expression in individual living cells.
A variety of tools and techniques can be employed to ...

Transposable elements (TEs) are genetic elements that mobilize within their host genomes by excision or catalyze copying followed by genomic reintegration. TEs exist in all domains of life, and transposition restructures the host genome, mutating coding and control regions1. This generates mutations and diversity that play an important role in evolution2,3, development4,5, and several human diseases6, including cancer7.
Using novel genetic constructs that couple aspects of transpositional activity to fluorescent reporters, our previous work described the development of an experimental system based on the bacterial TE IS608, a representative of the widespread IS200/IS605 family of TEs, that allows for the real-time visualization of transposition in individual live cells8 (Figure 1). The TE system is displayed in Figure 1A. The TE comprises the transposase coding sequence, tnpA, flanked by Left End (LE) and Right End (RE) imperfect palindromic repeats (IPs), which are the recognition and excision sites for TnpA. tnpA is expressed using the promoter PLTetO1, which is repressed by the tet repressor and is inducible with anhydrotetracycline (aTc)9. The TE splits the -10 and -35 sequences of a constitutive PlacIQ1 promoter10 for the blue reporter mCerulean311. As shown in Figure 1C, when the production of tnpA is induced, the TE can be excised, leading to promoter reconstitution. The produced cell expresses mCerulean3 and fluoresces blue. The N-terminus of TnpA is fused to the yellow reporter Venus12, allowing measurement of the TnpA levels by yellow fluorescence.
IS608 and other members of the IS200/IS605 family of transposons also typically encode a second gene of the thus far unknown function, tnpB13. The TnpB proteins are a tremendously abundant but imperfectly characterized family of nucleases encoded by several bacterial and archaeal TEs14,15, which often consist of only tnpB16. Furthermore, recent studies have renewed interest in TnpB by finding that TnpB functions as a CRISPR/Cas-like programmable RNA-guided endonuclease that will yield either dsDNA or ssDNA breaks under diverse conditions17,18. However, it remains unclear what role TnpB may play in regulating transposition. To perform real-time visualization of the effects of TnpB on IS608 transposition, a version of the transposon, including the coding region of TnpB with an N-terminal fusion to the red fluorescent protein mCherry, was created.
Complementing more detailed bulk-level studies performed by the Kuhlman lab19, it is shown here how real-time imaging of transposon activity can quantitatively reveal the impact of TnpB or any other accessory proteins on transpositional dynamics. By fusing TnpB to mCherry, the individual transpositional events are identified by blue fluorescence and correlated with expression levels of TnpA (yellow fluorescence) and TnpB (red fluorescence).

<table><tbody><tr><td>2 Ton Clear Epoxy</td><td>Devcon</td><td>31345</td><td></td></tr><tr><td>Agarose</td><td>Sigma-Aldrich</td><td>5066</td><td></td></tr><tr><td>Ammonium sulfate</td><td>Sigma-Aldrich</td><td>AX1385-1</td><td></td></tr><tr><td>Anhydrotetracycline hydrochloride</td><td>Sigma-Aldrich</td><td>37919</td><td></td></tr><tr><td>Argon Laser</td><td>Melles Griot</td><td>35-IMA-840-015</td><td></td></tr><tr><td>Blue Filter Cube</td><td>Chroma</td><td>Ex: Z457/10X, Em: ET485/30M</td><td></td></tr><tr><td>D(+)Glucose</td><td>Sigma-Aldrich</td><td>G7021</td><td></td></tr><tr><td>Eclipse Ti-E Microscope</td><td>Nikon</td><td></td><td>Discontinued</td></tr><tr><td>Eppendorf epTIPS Boxes and Refill Trays, Volume: 0.1 to 10 &amp;micro;L, Length: 3.4 cm, 1.33 in., PP (Polypropylene)</td><td>Eppendorf North America Biotools</td><td>22491504</td><td></td></tr><tr><td>Eppendorf epTIPS Boxes and Refill Trays, Volume: 50 to 1000 &amp;micro;L, Length: 7.1 cm, 2.79 in., PP (Polypropylene)</td><td>Eppendorf North America Biotools</td><td>22491555</td><td></td></tr><tr><td>Ferrous Sulfate Acs 500 g</td><td>Fisher Scientific</td><td>706834</td><td></td></tr><tr><td>Fiji</td><td></td><td></td><td>Fiji (imagej.net)</td></tr><tr><td>Fisher BioReagents&amp;nbsp;LB Broth, Miller (Granulated)</td><td>Fisher Scientific</td><td>BP9723-2&amp;nbsp;</td><td></td></tr><tr><td>Glass Cover Slide</td><td>Fisher Scientific</td><td>12-542B&amp;nbsp;</td><td></td></tr><tr><td>Kanamycin Sulfate</td><td>Sigma-Aldrich</td><td>1355006</td><td></td></tr><tr><td>Magnesium sulfate Cert Ac</td><td>Fisher Scientific</td><td>XXM63SP3KG</td><td></td></tr><tr><td>Microscope Heater</td><td>World Precision Instruments</td><td>96810-1</td><td></td></tr><tr><td>Potassium Phosphate Monobasic</td><td>Fisher Scientific</td><td>17001H</td><td></td></tr><tr><td>ProScan III Stage</td><td>Prior</td><td></td><td></td></tr><tr><td>Red Filter Cube</td><td>Chroma</td><td>Ex: ET560/40X, Em: ET645/75M</td><td></td></tr><tr><td>Sapphire 561 LP Laser</td><td>Coherent</td><td>1170412</td><td></td></tr><tr><td>Slide, Microscope</td><td>Fisher Scientific</td><td>125535B</td><td></td></tr><tr><td>Thiamine Hydrochloride</td><td>Sigma-Aldrich (SIAL)</td><td>T1270-100G</td><td></td></tr><tr><td>Ti-LU4 Laser Launch</td><td>Nikon</td><td></td><td></td></tr><tr><td>Yellow Filter Cube</td><td>Chroma</td><td>Ex: Z514/10X, Em: ET535/30M</td><td></td></tr></tbody></table>

real-time quantification of the effects of is200/is605 family-associated tnpb on transposon activity

Here, a protocol is outlined to perform live, real-time imaging of transposable element activity in live bacterial cells using a suite of fluorescent reporters coupled to transposition. In particular, it demonstrates how real-time imaging can be used to assess the effects of the accessory protein TnpB on the activity of the transposable element IS608, a member of the IS200/IS605 family of transposable elements. The IS200/IS605 family of transposable elements are abundant mobile elements connected with one of the most innumerable genes found in nature, tnpB. Sequence homologies propose that the TnpB protein may be an evolutionary precursor to CRISPR/Cas9 systems. Additionally, TnpB has received renewed interest, having been shown to act as a Cas-like RNA-guided DNA endonuclease. The effects of TnpB on the transposition rates of IS608 are quantified, and it is demonstrated that the expression of TnpB of IS608 results in ~5x increased transposon activity compared to cells lacking TnpB expression.

This method of visualizing transposon activity in live cells by fluorescence microscopy, while having lower throughput than bulk fluorescence measurements, allows direct visualization of transposon activity in individual live cells. Transposon excision events result in the reconstitution of the promoter for mCerulean3 (Figure 1), allowing identification of cells undergoing transposon activity by bright blue fluorescence (Figure 2, TnpB+: Supplementary Mo...

Watch this Scientific Journal Video about Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity at JoVE.com

Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity

A protocol is outlined to perform live real-time imaging to quantify how the accessory protein TnpB affects the dynamics of transposition in individual live Escherichia coli cells.

Here, a protocol is outlined to perform live, real-time imaging of transposable element activity in live bacterial cells using a suite of fluorescent ...

real-time-quantification-effects-is200is605-family-associated-tnpb-on

Research

JoVE Journal

Biology

2.3K Views.  University of California. Dit protocol stelt ons in staat om excisiestatistieken te kwantificeren op basis van één cel, in tegenstelling tot het kijken naar bulkgedrag. Op dit niveau kunnen we het gedrag van individuele cellen in de loop van de tijd volgen, inclusief hun TnpA- en TnpB-niveaus voor cellen die wegsnijden versus cellen die dat niet doen, waardoor we bijvoorbeeld de effecten van geïdentificeerde mutatiegebeurtenissen op de groeisnelheid kunnen meten. Deze methode is een eenvoudige, goedkope manier om d...

Video: Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity

Determination of the Optimal Chromosomal Location(s) for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach

The optimal chromosomal position(s) of a given DNA element was/were determined by transposon-mediated random insertion followed by fitness selection. In bacteria, the impact of the genetic context on the function of a genetic element can be difficult to assess. Several mechanisms, including topological effects, transcriptional interference from neighboring genes, and/or replication-associated gene dosage, may affect the function of a given genetic element. Here, we describe a method that permits the random integration of a DNA element into the chromosome of Escherichia coli and select the most favorable locations using a simple growth competition experiment. The method takes advantage of a well-described transposon-based system of random insertion, coupled with a selection of the fittest clone(s) by growth advantage, a procedure that is easily adjustable to experimental needs. The nature of the fittest clone(s) can be determined by whole-genome sequencing on a complex multi-clonal population or by easy gene walking for the rapid identification of selected clones. Here, the non-coding DNA region DARS2, which controls the initiation of chromosome replication in E. coli, was used as an example. The function of DARS2 is known to be affected by replication-associated gene dosage; the closer DARS2 gets to the origin of DNA replication, the more active it becomes. DARS2 was randomly inserted into the chromosome of a DARS2-deleted strain. The resultant clones containing individual insertions were pooled and competed against one another for hundreds of generations. Finally, the fittest clones were characterized and found to contain DARS2 inserted in close proximity to the original DARS2 location.

Determination of the Optimal Chromosomal Locations for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach

Here, the power of a transposon-mediated random insertion of a non-coding DNA element was used to resolve its optimal chromosomal position.

The optimal chromosomal position(s) of a given DNA element was/were determined by transposon-mediated random insertion followed by fitness selection. In ...

Genetics

Transient Expression of Foreign Genes in Insect Cells (sf9) for Protein Functional Assay

The transient gene expression system is one of the most important technologies for performing protein functional analysis in the baculovirus in vitro cell culture system. This system was developed to express foreign genes under the control of the baculoviral promoter in transient expression plasmids. Furthermore, this system can be applied to a functional assay of either the baculovirus itself or foreign proteins. The most widely and commercially available transient gene expression system is developed based on the immediate-early gene (IE) promoter of Orgyia pseudotsugata multicapsid nucleopolyhedrovirus (OpMNPV). However, a low expression level of foreign genes in insect cells was observed. Therefore, a transient gene expression system was constructed for improving protein expression. In this system, recombinant plasmids were constructed to contain the target sequence under the control of the Drosophila heat shock 70 (Dhsp70) promoter. This protocol presents the application of this heat shock-based pDHsp/V5-His (V5 epitope with 6 histidine)/Spodoptera frugiperda cell (sf9 cell) system; this system is available not only for gene expression but also for evaluating the anti-apoptotic activity of candidate proteins in insect cells. Furthermore, this system can be either transfected with one recombinant plasmid or co-transfected two potentially functionally antagonistic recombinant plasmids in insect cells. The protocol demonstrates the efficiency of this system and provides a practical case of this technique.

Transient Expression of Foreign Genes in Insect Cells sf9 for Protein Functional Assay

This protocol describes a heat shock-induced protein expression system (pDHsp/V5-His/sf9 cell system), which can be used for either expressing foreign proteins or evaluating the anti-apoptotic activity of potential foreign proteins and their truncated amino acids in insect cells.

The transient gene expression system is one of the most important technologies for performing protein functional analysis in the baculovirus in vitro cell ...

Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis

A central goal of modern genetics is to understand how and why organisms in the wild differ in phenotype. To date, the field has advanced largely on the strength of linkage and association mapping methods, which trace the relationship between DNA sequence variants and phenotype across recombinant progeny from matings between individuals of a species. These approaches, although powerful, are not well suited to trait differences between reproductively isolated species. Here we describe a new method for genome-wide dissection of natural trait variation that can be readily applied to incompatible species. Our strategy, RH-seq, is a genome-wide implementation of the reciprocal hemizygote test. We harnessed it to identify the genes responsible for the striking high temperature growth of the yeast Saccharomyces cerevisiae relative to its sister species S. paradoxus. RH-seq utilizes transposon mutagenesis to create a pool of reciprocal hemizygotes, which are then tracked through a high-temperature competition via high-throughput sequencing. Our RH-seq workflow as laid out here provides a rigorous, unbiased way to dissect ancient, complex traits in the budding yeast clade, with the caveat that resource-intensive deep sequencing is needed to ensure genomic coverage for genetic mapping. As sequencing costs drop, this approach holds great promise for future use across eukaryotes.

Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis

Reciprocal hemizygosity via sequencing (RH-seq) is a powerful new method to map the genetic basis of a trait difference between species. Pools of hemizygotes are generated by transposon mutagenesis and their fitness is tracked through competitive growth using high-throughout sequencing. Analysis of the resulting data pinpoints genes underlying the trait.

A central goal of modern genetics is to understand how and why organisms in the wild differ in phenotype. To date, the field has advanced largely on the ...

Applying an Inducible Expression System to Study Interference of Bacterial Virulence Factors with Intracellular Signaling

The technique presented here allows one to analyze at which step a target protein, or alternatively a small molecule, interacts with the components of a signaling pathway. The method is based, on the one hand, on the inducible expression of a specific protein to initiate a signaling event at a defined and predetermined step in the selected signaling cascade. Concomitant expression, on the other hand, of the gene of interest then allows the investigator to evaluate if the activity of the expressed target protein is located upstream or downstream of the initiated signaling event, depending on the readout of the signaling pathway that is obtained. Here, the apoptotic cascade was selected as a defined signaling pathway to demonstrate protocol functionality. Pathogenic bacteria, such as Coxiella burnetii, translocate effector proteins that interfere with host cell death induction in the host cell to ensure bacterial survival in the cell and to promote their dissemination in the organism. The C. burnetii effector protein CaeB effectively inhibits host cell death after induction of apoptosis with UV-light or with staurosporine. To narrow down at which step CaeB interferes with the propagation of the apoptotic signal, selected proteins with well-characterized pro-apoptotic activity were expressed transiently in a doxycycline-inducible manner. If CaeB acts upstream of these proteins, apoptosis will proceed unhindered. If CaeB acts downstream, cell death will be inhibited. The test proteins selected were Bax, which acts at the level of the mitochondria, and caspase 3, which is the major executioner protease. CaeB interferes with cell death induced by Bax expression, but not by caspase 3 expression. CaeB, thus, interacts with the apoptotic cascade between these two proteins.

The method described here is used to induce the apoptotic signaling cascade at defined steps in order to dissect the activity of an anti-apoptotic bacterial effector protein. This method can also be used for inducible expression of pro-apoptotic or toxic proteins, or for dissecting interference with other signaling pathways.

The technique presented here allows one to analyze at which step a target protein, or alternatively a small molecule, interacts with the components of a ...

Immunology and Infection

Creation of a Dense Transposon Insertion Library Using Bacterial Conjugation in Enterobacterial Strains Such As Escherichia Coli or Shigella flexneri

Transposon mutagenesis is a method that allows gene disruption via the random genomic insertion of a piece of DNA called a transposon. The protocol below outlines a method for high efficiency transfer between bacterial strains of a plasmid harboring a transposon containing a kanamycin resistance marker. The plasmid-borne transposase is encoded by a variant tnp gene that inserts the transposon into the genome of the recipient strain with very low insertional bias. This method thus allows the creation of large mutant libraries in which transposons have been inserted into unique genomic positions in a recipient strain of either Escherichia coli or Shigella flexneri bacteria. By using bacterial conjugation, as opposed to other methods such as electroporation or chemical transformation, large libraries with hundreds of thousands of unique clones can be created. This yields high-density insertion libraries, with insertions occurring as frequently as every 4-6 base pairs in non-essential genes. This method is superior to other methods as it allows for an inexpensive, easy to use, and high efficiency method for the creation of a dense transposon insertion library. The transposon library can be used in downstream applications such as transposon sequencing (Tn-Seq), to infer genetic interaction networks, or more simply, in mutational (forward genetic) screens.

Creation of a Dense Transposon Insertion Library Using Bacterial Conjugation in Enterobacterial Strains Such As Escherichia Coli or Shigella flexneri

Presented here is a simple method for creating a high-density transposon insertion library in Escherichia coli or Shigella flexneri using bacterial conjugation. This protocol allows the creation of a collection of hundreds of thousands of unique mutants in bacteria by the random genomic insertion of a transposon.

Transposon mutagenesis is a method that allows gene disruption via the random genomic insertion of a piece of DNA called a transposon. The protocol below ...

High-throughput Parallel Sequencing to Measure Fitness of Leptospira interrogans Transposon Insertion Mutants During Golden Syrian Hamster Infection

In this manuscript, we describe a transposon sequencing (Tn-Seq) technique to identify and quantify Leptospira interrogans mutants altered in fitness during infection of Golden Syrian hamsters. Tn-Seq combines random transposon mutagenesis with the power of high-throughput sequencing technology. Animals are challenged with a pool of transposon mutants (input pool), followed by harvesting of blood and tissues a few days later to identify and quantify the number of mutants in each organ (output pools). The output pools are compared to the input pool to evaluate the in vivo fitness of each mutant. This approach enables screening of a large pool of mutants in a limited number of animals. With minor modifications, this protocol can be performed with any animal model of leptospirosis, reservoir host models such as rats and acute infection models such as hamsters, as well as in vitro studies. Tn-Seq provides a powerful tool to screen for mutants with in vivo and in vitro fitness defects.

High-throughput Parallel Sequencing to Measure Fitness of Leptospira interrogans Transposon Insertion Mutants During Golden Syrian Hamster Infection

We describe here a technique that combines transposon mutagenesis with high-throughput sequencing to identify and quantify transposon leptospiral mutants in tissues after a challenge of hamsters. This protocol can be used to screen mutants for survival and dissemination in animals and can also be applied to in vitro studies.

In this manuscript, we describe a transposon sequencing (Tn-Seq) technique to identify and quantify Leptospira interrogans mutants altered in fitness ...

Replication of the Ordered, Nonredundant Library of Pseudomonas aeruginosa strain PA14 Transposon Insertion Mutants

Pseudomonas aeruginosa is a phenotypically and genotypically diverse and adaptable Gram-negative bacterium ubiquitous in human environments. P. aeruginosa is able to form biofilms, develop antibiotic resistance, produce virulence factors, and rapidly evolve in the course of a chronic infection. Thus P. aeruginosa can cause both acute and chronic, difficult to treat infections, resulting in significant morbidity in certain patient populations. P. aeruginosa strain PA14 is a human clinical isolate with a conserved genome structure that infects a variety of mammalian and nonvertebrate hosts making PA14 an attractive strain for studying this pathogen. In 2006, a nonredundant transposon insertion mutant library containing 5,459 mutants corresponding to 4,596 predicted PA14 genes was generated. Since then, distribution of the PA14 library has allowed the research community to better understand the function of individual genes and complex pathways of P. aeruginosa. Maintenance of library integrity through the replication process requires proper handling and precise techniques. To that end, this manuscript presents protocols that describe in detail the steps involved in library replication, library quality control and proper storage of individual mutants.

Replication of the Ordered, Nonredundant Library of Pseudomonas aeruginosa strain PA14 Transposon Insertion Mutants

Pseudomonas aeruginosa infection causes significant morbidity in vulnerable hosts. The nonredundant transposon insertion mutant library of P. aeruginosa strain PA14, designated as PA14NR Set, facilitates analysis of gene functionality in numerous processes. Presented here is a protocol to generate high-quality copies of the PA14NR Set mutant library.

Pseudomonas aeruginosa is a phenotypically and genotypically diverse and adaptable Gram-negative bacterium ubiquitous in human environments. P. aeruginosa ...

Generation of Enterobacter sp. YSU Auxotrophs Using Transposon Mutagenesis

Prototrophic bacteria grow on M-9 minimal salts medium supplemented with glucose (M-9 medium), which is used as a carbon and energy source. Auxotrophs can be generated using a transposome. The commercially available, Tn5-derived transposome used in this protocol consists of a linear segment of DNA containing an R6K&#947; replication origin, a gene for kanamycin resistance and two mosaic sequence ends, which serve as transposase binding sites. The transposome, provided as a DNA/transposase protein complex, is introduced by electroporation into the prototrophic strain, Enterobacter sp. YSU, and randomly incorporates itself into this host&#8217;s genome. Transformants are replica plated onto Luria-Bertani agar plates containing kanamycin, (LB-kan) and onto M-9 medium agar plates containing kanamycin (M-9-kan). The transformants that grow on LB-kan plates but not on M-9-kan plates are considered to be auxotrophs. Purified genomic DNA from an auxotroph is partially digested, ligated and transformed into a pir+ Escherichia coli (E. coli) strain. The R6K&#947; replication origin allows the plasmid to replicate in pir+ E. coli strains, and the kanamycin resistance marker allows for plasmid selection. Each transformant possesses a new plasmid containing the transposon flanked by the interrupted chromosomal region. Sanger sequencing and the Basic Local Alignment Search Tool (BLAST) suggest a putative identity of the interrupted gene. There are three advantages to using this transposome mutagenesis strategy. First, it does not rely on the expression of a transposase gene by the host. Second, the transposome is introduced into the target host by electroporation, rather than by conjugation or by transduction and therefore is more efficient. Third, the R6K&#947; replication origin makes it easy to identify the mutated gene which is partially recovered in a recombinant plasmid. This technique can be used to investigate the genes involved in other characteristics of Enterobacter sp. YSU or of a wider variety of bacterial strains.

Generation of Enterobacter sp. YSU Auxotrophs Using Transposon Mutagenesis

Enterobacter sp. YSU grows in glucose minimal salts medium. Auxotrophs are generated by transforming it with a transposome which randomly inserts itself into the host genome. Mutants are found by replica plating from complex medium to minimal medium. Interrupted genes are identified by gene rescue and sequencing.

Prototrophic bacteria grow on M-9 minimal salts medium supplemented with glucose (M-9 medium), which is used as a carbon and energy source. Auxotrophs can ...

An Efficient In Vitro Transposition Method by a Transcriptionally Regulated Sleeping Beauty System Packaged into an Integration Defective Lentiviral Vector

The Sleeping Beauty (SB) transposon is a non-viral integrating system with proven efficacy for gene transfer and functional genomics. To optimize the SB transposon machinery, a transcriptionally regulated hyperactive transposase (SB100X) and T2-based transposon are employed. Typically, the transposase and transposon are provided transiently by plasmid transfection and SB100X expression is driven by a constitutive promoter. Here, we describe an efficient method to deliver the SB components to human cells that are resistant to several physical and chemical transfection methods, to control SB100X expression and stably integrate a gene of interest (GOI) through a &#34;cut and paste&#34; SB mechanism. The expression of hyperactive transposase is tightly controlled by the Tet-ON system, widely used to control gene expression since 1992. The gene of interest is flanked by inverted repeats (IR) of the T2 transposon. Both SB components are packaged in integration defective lentiviral vectors transiently produced in HEK293T cells. Human cells, either cell lines or primary cells from human tissue, are in vitro transiently transduced with viral vectors. Upon addition of doxycycline (dox, tetracycline analog) into the culture medium, a fine-tuning of transposase expression is measured and results in a long-lasting integration of the gene of interest in the genome of the treated cells. This method is efficient and applicable to the cell line (e.g., HeLa cells) and primary cells (e.g., human primary keratinocytes), and thus represents a valuable tool for genetic engineering and therapeutic gene transfer.

An Efficient In Vitro Transposition Method by a Transcriptionally Regulated Sleeping Beauty System Packaged into an Integration Defective Lentiviral Vector

This protocol describes a method to achieve stable integration of a gene of interest into the human genome by the transcriptionally regulated Sleeping Beauty system. Preparation of the integration of defective lentiviral vectors, the in vitro transduction of human cells, and the molecular assay on transduced cells are reported.

The Sleeping Beauty (SB) transposon is a non-viral integrating system with proven efficacy for gene transfer and functional genomics. To optimize the SB ...

Generating Transposon Insertion Libraries in Gram-Negative Bacteria for High-Throughput Sequencing

Transposon sequencing (Tn-seq) is a powerful method that combines transposon mutagenesis and massive parallel sequencing to identify genes and pathways that contribute to bacterial fitness under a wide range of environmental conditions. Tn-seq applications are extensive and have not only enabled examination of genotype-phenotype relationships at an organism level but also at the population, community and systems levels. Gram-negative bacteria are highly associated with antimicrobial resistance phenotypes, which has increased incidents of antibiotic treatment failure. Antimicrobial resistance is defined as bacterial growth in the presence of otherwise lethal antibiotics. The &#8220;last-line&#8221; antimicrobial colistin is used to treat Gram-negative bacterial infections. However, several Gram-negative pathogens, including Acinetobacter baumannii can develop colistin resistance through a range of molecular mechanisms, some of which were characterized using Tn-seq. Furthermore, signal transduction pathways that regulate colistin resistance vary within Gram-negative bacteria. Here we propose an efficient method of transposon mutagenesis in A. baumannii that streamlines generation of a saturating transposon insertion library and amplicon library construction by eliminating the need for restriction enzymes, adapter ligation, and gel purification. The methods described herein will enable in-depth analysis of molecular determinants that contribute to A. baumannii fitness when challenged with colistin. The protocol is also applicable to other Gram-negative ESKAPE pathogens, which are primarily associated with drug resistant hospital-acquired infections.

We describe a method to generate saturating transposon mutant libraries in Gram-negative bacteria and subsequent preparation of DNA amplicon libraries for high-throughput sequencing. As an example, we focus on the ESKAPE pathogen, Acinetobacter baumannii, but this protocol is amenable to a wide range of Gram-negative organisms.

Transposon sequencing (Tn-seq) is a powerful method that combines transposon mutagenesis and massive parallel sequencing to identify genes and pathways ...

Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity

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