We thank Dr. Anders Omsland at Washington State University for supplying the CIP-1 axenic media. This work was supported by NIH grant R01AI130072, R21AI135691 and R21AI113617. Additional support was provided by startup funds from the University of Idaho and the Center for Modeling Complex Interactions through their NIH grant P20GM104420.

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	<li>AbdelRahman, Y., Belland, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+chlamydial+developmental+cycle.">The chlamydial developmental cycle.</a> FEMS Microbiology Reviews. 29 (5), 949-959 (2005).</li><li>Clifton, 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=A+chlamydial+type+III+translocated+protein+is+tyrosine-phosphorylated+at+the+site+of+entry+and+associated+with+recruitment+of+actin.">A chlamydial type III translocated protein is tyrosine-phosphorylated at the site of entry and associated with recruitment of actin.</a> Proceedings of the National Academy of Sciences U. S. A. 101 (27), 10166-10171 (2004).</li><li>Yu, H. H. Y., Tan, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=&#963;28+RNA+polymerase+regulates+hctB,+a+late+developmental+gene+in+Chlamydia.">&#963;28 RNA polymerase regulates hctB, a late developmental gene in Chlamydia.</a> Molecular Microbiology. 50 (2), 577-584 (2003).</li><li>Koo, I., Stephens, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Developmentally+Regulated+Two-component+Signal+Transduction+System+in+Chlamydia.">A Developmentally Regulated Two-component Signal Transduction System in Chlamydia.</a> Journal of Biological Chemistry. 278 (19), 17314-17319 (2003).</li><li>Grieshaber, 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=Impact+of+Active+Metabolism+on+Elementary+Body+Transcript+Profile+and+Infectivity.">Impact of Active Metabolism on Elementary Body Transcript Profile and Infectivity.</a> Journal of Bacteriology. 200 (14), 00065 (2018).</li><li>Belland, 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=Genomic+transcriptional+profiling+of+the+developmental+cycle+of.">Genomic transcriptional profiling of the developmental cycle of.</a> Proceedings of the National Academy of Sciences U. 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S. A. 109 (4), 1263-1268 (2012).</li><li>Mueller, K., Wolf, K., Fields, K., Maurelli, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gene+Deletion+by+Fluorescence-Reported+Allelic+Exchange+Mutagenesis+in+Chlamydia+trachomatis.">Gene Deletion by Fluorescence-Reported Allelic Exchange Mutagenesis in Chlamydia trachomatis.</a> MBio. 7 (1), 01817 (2016).</li><li>Rosario, C. J., Tan, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+early+gene+product+EUO+is+a+transcriptional+repressor+that+selectively+regulates+promoters+of+Chlamydia+late+genes.">The early gene product EUO is a transcriptional repressor that selectively regulates promoters of Chlamydia late genes.</a> Mol Microbiol. 84 (6), 1097-1107 (2012).</li><li>Brickman, T., Barry, C., Hackstadt, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+cloning+and+expression+of+hctB+encoding+a+strain-variant+chlamydial+histone-like+protein+with+DNA-binding+activity.">Molecular cloning and expression of hctB encoding a strain-variant chlamydial histone-like protein with DNA-binding activity.</a> Journal of Bacteriology. 175 (14), 4274-4281 (1993).</li><li>Omsland, A., Sager, J., Nair, V., Sturdevant, D., Hackstadt, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Developmental+stage-specific+metabolic+and+transcriptional+activity+of+Chlamydia+trachomatis+in+an+axenic+medium.">Developmental stage-specific metabolic and transcriptional activity of Chlamydia trachomatis in an axenic medium.</a> Proceedings of the National Academy of Sciences U. 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Y., 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=TrackMate:+An+open+and+extensible+platform+for+single-particle+tracking.">TrackMate: An open and extensible platform for single-particle tracking.</a> Methods. 115, 80-90 (2017).</li><li>Plotly Technologies Inc. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Collaborative data science. , (2015).</li><li>Lam, A. J., 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=Improving+FRET+dynamic+range+with+bright+green+and+red+fluorescent+proteins.">Improving FRET dynamic range with bright green and red fluorescent proteins.</a> Nature Methods. 9 (10), 1005-1012 (2012).</li><li>Shcherbo, 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=Far-red+fluorescent+tags+for+protein+imaging+in+living+tissues.">Far-red fluorescent tags for protein imaging in living tissues.</a> Biochemical Journal. 418 (3), 567-574 (2009).</li><li>Sega, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+review+of+the+genetic+effects+of+ethyl+methanesulfonate.">A review of the genetic effects of ethyl methanesulfonate.</a> Mutation Research. 134 (2-3), 113-142 (1984).</li><li>Ferguson, L., Denny, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Frameshift+mutagenesis+by+acridines+and+other+reversibly+binding+DNA+ligands.">Frameshift mutagenesis by acridines and other reversibly binding DNA ligands.</a> Mutagenesis. 5 (6), 529-540 (1990).</li></ol>

The authors have nothing to disclose.

Dissecting the mechanisms that control the chlamydial developmental cycle has been hindered by the limitations of the currently available genetic tools. Employing our promoter-reporter Chlamydia in conjunction with live-cell automated microscopy, a system was built which enables monitoring of cell-type development in individual inclusions over a 24 h period. This system, in combination with chemical mutagenesis and direct inclusion isolation has established a method to rapidly and clonally select Chlamydia</...

Chlamydia trachomatis (Ctr) is an obligate intracellular pathogen that progresses through a biphasic developmental cycle that is essential for its survival and proliferation1. This cycle consists of two developmental forms, the elementary body (EB) and the reticulate body (RB). The EB is replication incompetent but mediates cell invasion through effector induced endocytosis2. Once in the host, the EB matures to the replicative RB. The RB carries out multiple rounds of replication prior to converting back to the EB in order to initiate subsequent rounds of infection.
The limited array of genetic tools has restricted most of the chlamydial research to biochemical studies or the use of surrogate systems. As a consequence, elucidation of gene regulation and control of the developmental cycle has been difficult3,4. One of the more important challenges in the chlamydial field is the high resolution temporal tracking of the chlamydial developmental cycle and the identification of the proteins involved in its regulation. Gene expression during the chlamydial developmental cycle has traditionally been performed by destructive &#8220;end point&#8221; methods including RNAseq, qPCR, and fixed cell microscopy5,6. Although these methods have provided invaluable information, the techniques employed are laborious and have low temporal resolution5,6.
Within the last decade, genetic manipulation of Ctr has progressed with the introduction of plasmid transformation and methods for mutagenesis7,8,9. For this study, a plasmid-based system was developed to monitor chlamydial development in individual inclusions in real time over the course of an infection. A chlamydial transformant was created that expressed both an RB and EB cell-type specific promoter-reporter. The RB specific reporter was constructed by fusing the promoter of the early RB gene euo upstream of the fluorescent protein Clover. EUO is a transcriptional regulator that represses a subset of late EB associated genes10. The promoter of hctB, which encodes a histone-like protein involved in EB nucleoid condensation, was cloned directly upstream of mKate2 (RFP) to create the EB specific reporter11. The backbone for hctBprom-mKate2/euoprom-Clover was p2TK2SW27. The hctB and euo promoters were amplified from Ctr-L2 genomic DNA. Each promoter sequence consisted of ~100 base pairs upstream of the predicted transcription start site for the specified chlamydial gene plus the first 30 nucleotide (10 amino acids) of the respective ORF. The fluorescent FP variants were commercially obtained as Ctr codon optimized gene blocks and cloned in frame with the first 30 nucleotide of each chlamydial gene and promoter. The incD terminator was cloned directly downstream of mKate2. The second promoter-reporter was inserted downstream of the incD terminator. The ampicillin resistance gene (bla) in p2TK2SW2 was replaced with the aadA gene (Spectinomycin resistance) from pBam4. This resulted in the final construct p2TK2-hctBprom-mKate2/euoprom-Clover (Figure 1A) that was transformed into Ctr-L27. This RB/EB reporter strain allowed for the observation of the developmental cycle within single inclusions using live-cell microscopy (Figure 1B,C).
Employing our promoter-reporter construct in combination with chemical mutagenesis, a protocol was devised to track and isolate individual clones that exhibited developmental abnormalities from mutagenized populations of Ctr serovar L2. This protocol allows for the direct monitoring of individual chlamydial inclusions, tracking of the gene expression profiles over time, identifying chlamydial clones that express an altered developmental gene expression pattern, and clonal isolation of Chlamydia from individual inclusions.
Although this protocol has been created specifically for the identification of genes involved in chlamydial development, it could be easily adapted to interrogate any number of chlamydial genetic pathways.

<table><tbody><tr><td>24-well polystyrene plates</td><td>Corning</td><td>3524</td><td>Cell culture growth for reinfection of isolates</td></tr><tr><td>6-well glass bottom plates</td><td>Cellvis</td><td>P06-1.5H-N</td><td>Cell culture growth for imaging</td></tr><tr><td>96-well glass bottom plates</td><td>Nunc</td><td>165305</td><td>Cell culture growth for imaging</td></tr><tr><td>Bold line CO2 Unit</td><td>OKO Labs</td><td>CO2 UNIT BL</td><td>Stage incubator CO2 control</td></tr><tr><td>Bold line T Unit</td><td>OKO Labs</td><td>H301-T-UNIT-BL-PLUS</td><td>Stage incubator temperature control</td></tr><tr><td>Borosilicate glass capillary tubes</td><td>Sutter Instrument</td><td>B1005010</td><td>Capillary tubes</td></tr><tr><td>BrightLine bandpass emissions filter (514/30nm)</td><td>Semrock</td><td>FF01-514/30-25</td><td>Fluoescent filter cube</td></tr><tr><td>BrightLine bandpass emissions filter (641/75nm)</td><td>Semrock</td><td>FF02-641/75-25</td><td>Fluoescent filter cube</td></tr><tr><td>CellTram Vario</td><td>Eppendorf</td><td>5196000030</td><td>Microinjector</td></tr><tr><td>Chlamydia trachmatis serovar L2</td><td>ATCC</td><td>VR-577</td><td>Chlamydia trachomatis</td></tr><tr><td>CIP-1 media</td><td>In house</td><td>NA</td><td>Axenic media. IPB supplemented with 1% FBS, 25 &amp;mu;M amino acids, 0.5&lt;br/&gt; mM G6P, 1.0 mM ATP, 0.5 mM DTT, and 50 &amp;mu;M GTP, UTP, and&lt;br/&gt; CTP. (Omsland, A. 2012) made in-house.</td></tr><tr><td>Cos-7 cells (ATCC)</td><td>ATCC</td><td>CRL-1651</td><td>African green monkey kidney cell (host cells)</td></tr><tr><td>Cycloheximide</td><td>MP Biomedicals</td><td>194527</td><td>Host cell growth inhibitor</td></tr><tr><td>Ethyl methanesulfonate, 99%</td><td>Acros Organics</td><td>AC205260100</td><td>Mutagen</td></tr><tr><td>Fetal Plex</td><td>Gemini Bio-Products</td><td>100-602</td><td>Supplement for base growth media</td></tr><tr><td>Fiji/ImageJ</td><td>&lt;u&gt;https://imagej.net/Fiji&lt;/u&gt;</td><td>NA</td><td>Open sourse Image analysis software. https://imagej.net/Fiji</td></tr><tr><td>Galaxy 170 S CO2 incubator</td><td>Eppendorf</td><td>CO1700100X</td><td>Cell culture incubation</td></tr><tr><td>gblocks (Fluorescent FP variants: Clover and mKate2)</td><td>Integrated DNA Technologies</td><td>NA</td><td>gblock ORFs of Ctr optimized FP varients for cloning into p2TK2SW2</td></tr><tr><td>Gentamycin 10mg/ml</td><td>Gibco</td><td>15710-064</td><td>Antibiotic for growth media</td></tr><tr><td>HBSS (Hank&#039;s Balanced Salt Solution)</td><td>Corning</td><td>21-020-CM</td><td>Host cells rinse</td></tr><tr><td>Heparin sodium</td><td>Amersham Life Science</td><td>16920</td><td>inhibits and reverses the early electrostatic interactions between the host cell and EBs</td></tr><tr><td>HEPES 1M</td><td>GE Life Sciences</td><td>SH30237.01</td><td>pH buffer for growth media</td></tr><tr><td>InjectMan</td><td>Eppendorf</td><td>5179 000.018</td><td>Micromanipulator</td></tr><tr><td>Jupyter Notebook</td><td>&lt;u&gt;https://jupyter.org/&lt;/u&gt;</td><td>NA</td><td>Visualization of inclusion traces. https://jupyter.org/</td></tr><tr><td>Lambda 10-3</td><td>Sutter Instrument</td><td>LB10-3</td><td>Filter wheel controler</td></tr><tr><td>Oko Touch</td><td>OKO Labs</td><td>Oko Touch</td><td>Interface to control the Bold line T and CO2 Unit</td></tr><tr><td>Prior XY stage</td><td>Prior</td><td>H107</td><td>Motorized XY microscope stage</td></tr><tr><td>PrismR Centrifuge</td><td>Labnet</td><td>C2500-R</td><td>Temperature controlled microcentrifuge</td></tr><tr><td>Problot Hybridization oven</td><td>Labnet</td><td>H1200A</td><td>Rocking Incubator for infection with Chlamydia</td></tr><tr><td>Proscan II</td><td>Prior</td><td>H30V4</td><td>XYZ microscope stage controler</td></tr><tr><td>Purifier Class 2 Biosafety Cabinet</td><td>Labconco</td><td>362804</td><td>Cell culture work</td></tr><tr><td>RPMI-1640 (no phenol red)</td><td>Gibco</td><td>11835-030</td><td>Base growth media for imaging</td></tr><tr><td>RPMI-1640 (phenol red)</td><td>GE Life Sciences</td><td>SH30027.01</td><td>Base growth media</td></tr><tr><td>scopeLED excitation LEDs (470nm,595nm)</td><td>scopeLED</td><td>F140</td><td>Excitation light</td></tr><tr><td>Sonic Dismembrator Model 500</td><td>Fisher Scientific</td><td>15-338-550</td><td>Sonicator, resuspending chlamydial pellet</td></tr><tr><td>Stage incubator</td><td>OKO Labs</td><td>H301-K-FRAME</td><td>Cluster well plate incubation chamber</td></tr><tr><td>sucrose-phosphate-glutamate buffer 1X (SPG)</td><td>In house</td><td>NA</td><td>Chlamydial storage buffer. (10 mM sodium phosphate [8 mM K 2HPO 4, 2 mM KH 2PO 4], 220 mM sucrose, 0.50 mM L-glutamic acid; pH 7.4)</td></tr><tr><td>T-75 Flasks</td><td>Thermo Scientific</td><td>156499</td><td>Cell culture growth</td></tr><tr><td>TE 300 inverted microscope</td><td>Nikon</td><td>16724</td><td>microscope</td></tr><tr><td>THOR LED</td><td>Thor Labs</td><td>LEDD1B</td><td>White light</td></tr><tr><td>Trypsin</td><td>Corning</td><td>25-052-CI</td><td>Dislodges host cells from flask for seeding into plates</td></tr><tr><td>Zyla sCMOS</td><td>Andor</td><td>ZYLA-5.5-USB3</td><td>imaging camera</td></tr><tr><td>&amp;micro;Manager 2.0gamma</td><td>&lt;u&gt;https://github.com/micro-manager/micro-manager&lt;/u&gt;</td><td>NA</td><td>Open sourse automated microscope control software package</td></tr></tbody></table>

live-cell forward genetic approach to identify and isolate developmental mutants in chlamydia trachomatis

The intracellular bacterial pathogen Chlamydia trachomatis undergoes a developmental cycle consisting of two morphologically discrete developmental forms. The non-replicative elementary body (EB) initiates infection of the host. Once inside, the EB differentiates into the reticulate body (RB). The RB then undergoes multiple rounds of replication, before differentiating back to the infectious EB form. This cycle is essential for chlamydial survival as failure to switch between cell types prevents either host invasion or replication.
Limitations in genetic techniques due to the obligate intracellular nature of Chlamydia have hampered identification of the molecular mechanisms involved in the cell-type development. We designed a novel dual promoter-reporter plasmid system that, in conjunction with live-cell microscopy, allows for the visualization of cell type switching in real time. To identify genes involved in the regulation of cell-type development, the live-cell promoter-reporter system was leveraged for the development of a forward genetic approach by combining chemical mutagenesis of the dual reporter strain, imaging and tracking of Chlamydia with altered developmental kinetics, followed by clonal isolation of mutants. This forward genetic workflow is a flexible tool that can be modified for directed interrogation into a wide range of genetic pathways.

Direct EMS mutagenesis of our promoter-reporter chlamydial strain resulted in an ~75% reduction in infectivity. Using the described live-cell imaging protocol, ~600 inclusions were imaged and tracked over a 24 h period. The fluorescent expression kinetics of both reporters in each inclusion was visualized using custom Python notebook scripts. Two visualization approaches were implemented to identify candidate mutagenized Chlamydia for isolation. The first methodology (step 3.3.8) visualizes the time to half-maxi...

Watch this Scientific Journal Video about Live-Cell Forward Genetic Approach to Identify and Isolate Developmental Mutants in Chlamydia trachomatis at JoVE.com

Live-Cell Forward Genetic Approach to Identify and Isolate Developmental Mutants in Chlamydia trachomatis

This protocol utilizes fluorescent promoter-reporters, live-cell microscopy, and individual inclusion extraction in a directed forward genetic approach to identify and isolate developmental mutants of Chlamydia trachomatis.

Live-Cell Forward Genetic Approach to Identify and Isolate Developmental Mutants in Chlamydia trachomatis

The intracellular bacterial pathogen Chlamydia trachomatis undergoes a developmental cycle consisting of two morphologically discrete developmental forms. ...

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Immunology and Infection

4.2K Views.  University of Idaho. This protocol utilizes fluorescent promoter-reporters, live-cell microscopy, and individual inclusion extraction in a directed forward genetic approach to identify and isolate developmental mutants of Chlamydia trachomatis.

Video: Live-Cell Forward Genetic Approach to Identify and Isolate Developmental Mutants in Chlamydia trachomatis

High-Throughput Robotically Assisted Isolation of Temperature-sensitive Lethal Mutants in Chlamydomonas reinhardtii

Systematic identification and characterization of genetic perturbations have proven useful to decipher gene function and cellular pathways. However, the conventional approaches of permanent gene deletion cannot be applied to essential genes. We have pioneered a unique collection of ~70 temperature-sensitive (ts) lethal mutants for studying cell cycle regulation in the unicellular green algae Chlamydomonas reinhardtii1. These mutations identify essential genes, and the ts alleles can be conditionally inactivated by temperature shift, providing valuable tools to identify and analyze essential functions. Mutant collections are much more valuable if they are close to comprehensive, since scattershot collections can miss important components. However, this requires the efficient collection of a large number of mutants, especially in a wide-target screen. Here, we describe a robotics-based pipeline for generating ts lethal mutants and analyzing their phenotype in Chlamydomonas. This technique can be applied to any microorganism that grows on agar. We have collected over 3000 ts mutants, probably including mutations in most or all cell-essential pathways, including about 200 new candidate cell cycle mutations. Subsequent molecular and cellular characterization of these mutants should provide new insights in plant cell biology; a comprehensive mutant collection is an essential prerequisite to ensure coverage of a broad range of biological pathways. These methods are integrated with downstream genetics and bioinformatics procedures for efficient mapping and identification of the causative mutations that are beyond the scope of this manuscript.

High-Throughput Robotically Assisted Isolation of Temperature-sensitive Lethal Mutants in Chlamydomonas reinhardtii

Temperature-sensitive (ts) lethal mutants are valuable tools to identify and analyze essential functions. Here we describe methods to generate and classify ts lethal mutants in high throughput.

Systematic identification and characterization of genetic perturbations have proven useful to decipher gene function and cellular pathways. However, the ...

Genetics

A Genetic Screen to Isolate Toxoplasma gondii Host-cell Egress Mutants

The widespread, obligate intracellular, protozoan parasite Toxoplasma gondii causes opportunistic disease in immuno-compromised patients and causes birth defects upon congenital infection. The lytic replication cycle is characterized by three stages: 1. active invasion of a nucleated host cell; 2. replication inside the host cell; 3. active egress from the host cell. The mechanism of egress is increasingly being appreciated as a unique, highly regulated process, which is still poorly understood at the molecular level. The signaling pathways underlying egress have been characterized through the use of pharmacological agents acting on different aspects of the pathways1-5. As such, several independent triggers of egress have been identified which all converge on the release of intracellular Ca2+, a signal that is also critical for host cell invasion6-8. This insight informed a candidate gene approach which led to the identification of plant like calcium dependent protein kinase (CDPK) involved in egress9. In addition, several recent breakthroughs in understanding egress have been made using (chemical) genetic approaches10-12. To combine the wealth of pharmacological information with the increasing genetic accessibility of Toxoplasma we recently established a screen permitting the enrichment for parasite mutants with a defect in host cell egress13. Although chemical mutagenesis using N-ethyl-N-nitrosourea (ENU) or ethyl methanesulfonate (EMS) has been used for decades in the study of Toxoplasma biology11,14,15, only recently has genetic mapping of mutations underlying the phenotypes become routine16-18. Furthermore, by generating temperature-sensitive mutants, essential processes can be dissected and the underlying genes directly identified. These mutants behave as wild-type under the permissive temperature (35 &deg;C), but fail to proliferate at the restrictive temperature (40 &deg;C) as a result of the mutation in question. Here we illustrate a new phenotypic screening method to isolate mutants with a temperature-sensitive egress phenotype13. The challenge for egress screens is to separate egressed from non-egressed parasites, which is complicated by fast re-invasion and general stickiness of the parasites to host cells. A previously established egress screen was based on a cumbersome series of biotinylation steps to separate intracellular from extracellular parasites11. This method also did not generate conditional mutants resulting in weak phenotypes. The method described here overcomes the strong attachment of egressing parasites by including a glycan competitor, dextran sulfate (DS), that prevents parasites from sticking to the host cell19. Moreover, extracellular parasites are specifically killed off by pyrrolidine dithiocarbamate (PDTC), which leaves intracellular parasites unharmed20. Therefore, with a new phenotypic screen to specifically isolate parasite mutants with defects in induced egress, the power of genetics can now be fully deployed to unravel the molecular mechanisms underlying host cell egress.

A Genetic Screen to Isolate Toxoplasma gondii Host-cell Egress Mutants

Forward genetics is a powerful method to unravel the molecular level of how Toxoplasma egresses from its host cell. Protocols are provided to chemically mutagenize parasites, enrich for mutants with defects in induced egress, and validate the phenotype of cloned mutants.

The widespread, obligate intracellular, protozoan parasite Toxoplasma gondii causes opportunistic disease in immuno-compromised patients and causes birth ...

Live-cell Video Microscopy of Fungal Pathogen Phagocytosis

Phagocytic clearance of fungal pathogens, and microorganisms more generally, may be considered to consist of four distinct stages: (i) migration of phagocytes to the site where pathogens are located; (ii) recognition of pathogen-associated molecular patterns (PAMPs) through pattern recognition receptors (PRRs); (iii) engulfment of microorganisms bound to the phagocyte cell membrane, and (iv) processing of engulfed cells within maturing phagosomes and digestion of the ingested particle. Studies that assess phagocytosis in its entirety are informative1, 2, 3, 4, 5 but are limited in that they do not normally break the process down into migration, engulfment and phagosome maturation, which may be affected differentially. Furthermore, such studies assess uptake as a single event, rather than as a continuous dynamic process. We have recently developed advanced live-cell imaging technologies, and have combined these with genetic functional analysis of both pathogen and host cells to create a cross-disciplinary platform for the analysis of innate immune cell function and fungal pathogenesis. These studies have revealed novel aspects of phagocytosis that could only be observed using systematic temporal analysis of the molecular and cellular interactions between human phagocytes and fungal pathogens and infectious microorganisms more generally. For example, we have begun to define the following: (a) the components of the cell surface required for each stage of the process of recognition, engulfment and killing of fungal cells1, 6, 7, 8; (b) how surface geometry influences the efficiency of macrophage uptake and killing of yeast and hyphal cells7; and (c) how engulfment leads to alteration of the cell cycle and behavior of macrophages 9, 10.
In contrast to single time point snapshots, live-cell video microscopy enables a wide variety of host cells and pathogens to be studied as continuous sequences over lengthy time periods, providing spatial and temporal information on a broad range of dynamic processes, including cell migration, replication and vesicular trafficking. Here we describe in detail how to prepare host and fungal cells, and to conduct the video microscopy experiments. These methods can provide a user-guide for future studies with other phagocytes and microorganisms.

We describe methods for live-cell video microscopy of Candida albicans phagocytosis by macrophages. These methods enable stage-specific analysis of macrophage migration, recognition, engulfment and phagosome maturation and reveal novel aspects of phagocytosis.

Phagocytic clearance of fungal pathogens, and microorganisms more generally, may be considered to consist of four distinct stages: (i) migration of ...

Identification of Host Pathways Targeted by Bacterial Effector Proteins using Yeast Toxicity and Suppressor Screens

Intracellular bacteria secrete virulence factors called effector proteins into the host cytosol that act to subvert host proteins and/or their associated biological pathways to the benefit of the bacterium. Identification of putative bacterial effector proteins has become more manageable due to advances in bacterial genome sequencing and the advent of algorithms that allow in silico identification of genes encoding secretion candidates and/or eukaryotic-like domains. However, identification of these important virulence factors is only an initial step. Naturally, the goal is to determine the molecular function of effector proteins and elucidate how they interact with the host. In recent years, techniques like the yeast two-hybrid screen and large-scale immunoprecipitations coupled with mass spectrometry have aided in the identification of protein-protein interactions. Although identification of a host binding partner is the crucial first step toward elucidating the molecular function of a bacterial effector protein, sometimes the host protein is found to have multiple biological functions (e.g., actin, clathrin, tubulin), or the bacterial protein may not physically bind host proteins, depriving the researcher of crucial information about the precise host pathway being manipulated. A modified yeast toxicity screen coupled with a suppressor screen has been adapted to identify host pathways impacted by bacterial effector proteins. The toxicity screen relies on a toxic effect in yeast caused by the effector protein interfering with the host biological pathways, which often manifests as a growth defect. Expression of a yeast genomic library is used to identify host factors that suppress the toxicity of the bacterial effector protein and thus identify proteins in the pathway that the effector protein targets. This protocol contains detailed instructions for both the toxicity and suppressor screens. These techniques can be performed in any lab capable of molecular cloning and cultivation of yeast and Escherichia coli.

Bacterial pathogens secrete proteins into the host that target crucial biological processes. Identifying the host pathways targeted by bacterial effector proteins is key to addressing molecular pathogenesis. Here, a method using a modified yeast suppressor and toxicity screen to elucidate host pathways targeted by toxic bacterial effector proteins is described.

Intracellular bacteria secrete virulence factors called effector proteins into the host cytosol that act to subvert host proteins and/or their associated ...

Forward Genetic Approaches in Chlamydia trachomatis

Chlamydia trachomatis, the etiological agent of sexually transmitted diseases and ocular infections, remains poorly characterized due to its intractability to experimental transformation with recombinant DNA. We developed an approach to perform genetic analysis in C. trachomatis&#160;despite the lack of molecular genetic tools. Our method involves: i.) chemical mutagenesis to rapidly generate comprehensive libraries of genetically-defined mutants with distinct phenotypes; ii.) whole-genome sequencing (WGS) to map the underlying genetic lesions and to find associations between mutated gene(s) and a common phenotype; iii.) generation of recombinant strains through co-infection of mammalian cells with mutant and wild type bacteria. Accordingly, we were able to establish causal relationships between genotypes and phenotypes. The coupling of chemically-induced gene variation and WGS to establish correlative genotype&#8211;phenotype associations should be broadly applicable to the large list of medically and environmentally important microorganisms currently intractable to genetic analysis.

Forward Genetic Approaches in Chlamydia trachomatis

We describe a methodology to perform genetic analysis in Chlamydia based on chemical mutagenesis and whole genome sequencing. In addition, a system for DNA exchange within infected cells is described that can be used for genetic mapping. This method may be broadly applicable to microbial systems lacking transformation systems and molecular genetic tools.

Chlamydia trachomatis, the etiological agent of sexually transmitted diseases and ocular infections, remains poorly characterized due to its ...

Using Fluorescent Proteins to Visualize and Quantitate Chlamydia Vacuole Growth Dynamics in Living Cells

The obligate intracellular bacterium Chlamydia elicits a great burden on global public health. C.&#160;trachomatis is the leading bacterial cause of sexually transmitted infection and also the primary cause of preventable blindness in the world. An essential determinant for successful infection of host cells by Chlamydia is the bacterium's ability to manipulate host cell signaling from within a novel, vacuolar compartment called the inclusion. From within the inclusion, Chlamydia acquire nutrients required for their 2-3 day developmental growth, and they additionally secrete a panel of effector proteins onto the cytosolic face of the vacuole membrane and into the host cytosol. Gaps in our understanding of Chlamydia biology, however, present significant challenges for visualizing and analyzing this intracellular compartment. Recently, a reverse-imaging strategy for visualizing the inclusion using GFP expressing host cells was described. This approach rationally exploits the intrinsic impermeability of the inclusion membrane to large molecules such as GFP. In this work, we describe how GFP- or mCherry-expressing host cells are generated for subsequent visualization of chlamydial inclusions. Furthermore, this method is shown to effectively substitute for costly antibody-based enumeration methods, can be used in tandem with other fluorescent labels, such as GFP-expressing Chlamydia, and can be exploited to derive key quantitative data about inclusion membrane growth from a range of Chlamydia species and strains.

Using Fluorescent Proteins to Visualize and Quantitate Chlamydia Vacuole Growth Dynamics in Living Cells

A live cell fluorescent protein based method for illuminating cellular vacuoles (inclusions) containing Chlamydia is described. This strategy enables rapid, automated determination of Chlamydia infectivity in samples and can be used to quantitatively investigate inclusion growth dynamics.

The obligate intracellular bacterium Chlamydia elicits a great burden on global public health. C.&#160;trachomatis is the leading bacterial cause of ...

Forward Genetics Screens Using Macrophages to Identify Toxoplasma gondii Genes Important for Resistance to IFN-&#947;-Dependent Cell Autonomous Immunity

Toxoplasma gondii, the causative agent of toxoplasmosis, is an obligate intracellular protozoan pathogen. The parasite invades and replicates within virtually any warm blooded vertebrate cell type. During parasite invasion of a host cell, the parasite creates a parasitophorous vacuole (PV) that originates from the host cell membrane independent of phagocytosis within which the parasite replicates. While IFN-dependent-innate and cell mediated immunity is important for eventual control of infection, innate immune cells, including neutrophils, monocytes and dendritic cells, can also serve as vehicles for systemic dissemination of the parasite early in infection. An approach is described that utilizes the host innate immune response, in this case macrophages, in a forward genetic screen to identify parasite mutants with a fitness defect in infected macrophages following activation but normal invasion and replication in na&#239;ve macrophages. Thus, the screen isolates parasite mutants that have a specific defect in their ability to resist the effects of macrophage activation. The paper describes two broad phenotypes of mutant parasites following activation of infected macrophages: parasite stasis versus parasite degradation, often in amorphous vacuoles. The parasite mutants are then analyzed to identify the responsible parasite genes specifically important for resistance to induced mediators of cell autonomous immunity. The paper presents a general approach for the forward genetics screen that, in theory, can be modified to target parasite genes important for resistance to specific antimicrobial mediators. It also describes an approach to evaluate the specific macrophage antimicrobial mediators to which the parasite mutant is susceptible. Activation of infected macrophages can also promote parasite differentiation from the tachyzoite to bradyzoite stage that maintains chronic infection. Therefore, methodology is presented to evaluate the importance of the identified parasite gene to establishment of chronic infection.

Forward Genetics Screens Using Macrophages to Identify Toxoplasma gondii Genes Important for Resistance to IFN-&#947;-Dependent Cell Autonomous Immunity

Forward genetics is a powerful approach to identify genes in intracellular pathogens important for resistance to cell autonomous immunity. The current approach uses innate immune cells, specifically macrophages, to identify novel Toxoplasma gondii genes important for immune evasion.

Toxoplasma gondii, the causative agent of toxoplasmosis, is an obligate intracellular protozoan pathogen. The parasite invades and replicates within ...

A Simple and Efficient Approach to Construct Mutant Vaccinia Virus Vectors

The CRISPR-associated endonuclease Cas9 can edit particular genomic loci directed by a single guide RNA (gRNA). The CRISPR/Cas9 system has been successfully employed for editing genomes of various organisms. Here we describe a protocol for editing the vaccinia virus (VV) genome in the cytoplasm of VV-infected CV-1 cells using the RNA-guided Cas9. RNA-guided Cas9 induces double-stranded DNA breaks facilitating homologous recombination efficiently and specifically in the targeted site of VV and a transgene can be incorporated into these sites by homologous recombination. By using a site-specific homologous vector with transgene(s), a N1L gene-deleted VV with the red fluorescence protein (RFP) gene incorporated in this region was generated with a successful recombination efficiency 10 times greater than that obtained from the conventional homologous recombination method. This protocol demonstrates successful use of RNA-guided Cas9 system to generate mutant VVs with enhanced efficiency.

Vaccinia virus (VV) has been widely used in biomedical research and the improvement of human health. This article describes a simple, highly efficient method to edit the VV genome using a CRISPR-Cas9 system.

The CRISPR-associated endonuclease Cas9 can edit particular genomic loci directed by a single guide RNA (gRNA). The CRISPR/Cas9 system has been ...

Retroviral Transduction of Helper T Cells as a Genetic Approach to Study Mechanisms Controlling their Differentiation and Function

Helper T cell development and function must be tightly regulated to induce an appropriate immune response that eliminates specific pathogens yet prevents autoimmunity. Many approaches involving different model organisms have been utilized to understand the mechanisms controlling helper T cell development and function. However, studies using mouse models have proven to be highly informative due to the availability of genetic, cellular, and biochemical systems. One genetic approach in mice used by many labs involves retroviral transduction of primary helper T cells. This is a powerful approach due to its relative ease, making it accessible to almost any laboratory with basic skills in molecular biology and immunology. Therefore, multiple genes in wild type or mutant forms can readily be tested for function in helper T cells to understand their importance and mechanisms of action. We have optimized this approach and describe here the protocols for production of high titer retroviruses, isolation of primary murine helper T cells, and their transduction by retroviruses and differentiation toward the different helper subsets. Finally, the use of this approach is described in uncovering mechanisms utilized by microRNAs (miRNAs) to regulate pathways controlling helper T cell development and function.

Many experimental systems have been utilized to understand the mechanisms regulating T cell development and function in an immune response. Here a genetic approach using retroviral transduction is described, which is economic, time efficient, and most importantly, highly informative in identifying regulatory pathways.

Helper T cell development and function must be tightly regulated to induce an appropriate immune response that eliminates specific pathogens yet prevents ...

Markerless Gene Deletion by Floxed Cassette Allelic Exchange Mutagenesis in Chlamydia trachomatis

Chlamydia trachomatis is an obligate intracellular pathogen that has been historically difficult to genetically manipulate. Definitive progress in elucidating the mechanisms that C. trachomatis use to create and maintain a privileged intracellular niche has been limited due to a lack of genetic tools. Fortunately, there have recently been several new advances in genetic manipulation techniques. Among these is the development of fluorescence-reported allelic exchange mutagenesis (FRAEM). This method allows targeted gene deletion coupled with insertion of a selection cassette encoding antibiotic resistance and green fluorescent protein (GFP). Reliance on this strategy can be complicated when targeting genes within polycistronic operons due to the potential of polar effects on downstream genes. Floxed cassette allelic exchange mutagenesis (FLAEM), the protocol for which is described here, was developed to alleviate cassette-induced polar effects. FLAEM utilizes Cre-loxP genome editing to remove the selection cassette after targeted deletion by allelic exchange. The resulting strains contain markerless gene deletions of one or more coding sequences. This technique facilitates direct assessment of gene function and expands the repertoire of tools for genetic manipulation in C. trachomatis.

Markerless Gene Deletion by Floxed Cassette Allelic Exchange Mutagenesis in Chlamydia trachomatis

Described here is a method for targeted, markerless gene deletion in Chlamydia trachomatis using floxed cassette allelic exchange mutagenesis, FLAEM.

Live-Cell Forward Genetic Approach to Identify and Isolate Developmental Mutants in Chlamydia trachomatis

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Chapters in this video

High-Throughput Robotically Assisted Isolation of Temperature-sensitive Lethal Mutants in Chlamydomonas reinhardtii

A Genetic Screen to Isolate Toxoplasma gondii Host-cell Egress Mutants

Live-cell Video Microscopy of Fungal Pathogen Phagocytosis

Identification of Host Pathways Targeted by Bacterial Effector Proteins using Yeast Toxicity and Suppressor Screens

Forward Genetic Approaches in Chlamydia trachomatis

Using Fluorescent Proteins to Visualize and Quantitate Chlamydia Vacuole Growth Dynamics in Living Cells

Forward Genetics Screens Using Macrophages to Identify Toxoplasma gondii Genes Important for Resistance to IFN-γ-Dependent Cell Autonomous Immunity

A Simple and Efficient Approach to Construct Mutant Vaccinia Virus Vectors

Retroviral Transduction of Helper T Cells as a Genetic Approach to Study Mechanisms Controlling their Differentiation and Function

Markerless Gene Deletion by Floxed Cassette Allelic Exchange Mutagenesis in Chlamydia trachomatis