Name: high-resolution comparison of bacterial conjugation frequencies
Uploaded: 2019-01-10T13:00:00
Description: Watch this Scientific Journal Video about High-Resolution Comparison of Bacterial Conjugation Frequencies at JoVE.com

We thank Dr. K. Kamachi of the National Institute of Infectious Diseases (Japan) for providing pBP136 and Prof. Dr. H. Nojiri of the University of Tokyo (Japan) for providing pCAR1. We are also grateful to Professor Dr. Molin S&#248;len of the Technical University of Denmark for providing pJBA28. This work was supported by JSPS KAKENHI (Grant Numbers 15H05618 and 15KK0278) to MS (https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-15H05618/, https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-15KK0278/).

1. Preparation of a Donor with Green Fluorescent Protein (GFP)- and Kanamycin Resistance Gene-Tagged Plasmids
<ol>
	<li>Introduction of marker genes into the target plasmid pBP136 
	Note: The goal of this protocol is to generate pBP136::gfp. The bacterial strains and plasmids used in this study are listed in Table 1.
	<ol>
		<li>Grow cultures of Escherichia coli DH10B harboring pBP13617 in 5 mL of sterile Luria br...

<ol>
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K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effect+of+ecological+factors+on+conjugal+transfer+of+chromium-resistant+plasmid+in+Escherichia+coli+isolated+from+tannery+effluent.">Effect of ecological factors on conjugal transfer of chromium-resistant plasmid in Escherichia coli isolated from tannery effluent.</a> Biotechnology and Applied Biochemistry. 102 (1-6), 5-20 (2002).</li><li>Sakuda, 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=Divalent+cations+increase+the+conjugation+efficiency+of+the+incompatibility+P-7+group+plasmid+pCAR1+among+different+Pseudomonas+hosts.">Divalent cations increase the conjugation efficiency of the incompatibility P-7 group plasmid pCAR1 among different Pseudomonas hosts.</a> Microbiology. 164 (1), 20-27 (2018).</li><li>Corliss, T. L., Cohen, P. S., Cabelli, V. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=R-plasmid+transfer+to+and+from+Escherichia+coli+strains+Isolated+from+human+fecal+samples.">R-plasmid transfer to and from Escherichia coli strains Isolated from human fecal samples.</a> Applied and Environmental Microbiology. 41 (4), 959-966 (1981).</li><li>Zhong, X., Krol, J. E., Top, E. M., Krone, S. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Accounting+for+mating+pair+formation+in+plasmid+population+dynamics.">Accounting for mating pair formation in plasmid population dynamics.</a> Journal of Theoretical Biology. 262 (4), 711-719 (2010).</li><li>Gilmour, M. W., Lawley, T. D., Taylor, D. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+cytology+of+bacterial+conjugation.">The cytology of bacterial conjugation.</a> EcoSal Plus. 2004, (2004).</li><li>Minoia, M., 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=Stochasticity+and+bistability+in+horizontal+transfer+control+of+a+genomic+island+in+Pseudomonas.">Stochasticity and bistability in horizontal transfer control of a genomic island in Pseudomonas.</a> Proceedings of the National Academy of Sciences of the United States of America. 105 (52), 20792-20797 (2008).</li><li>Kamachi, K., 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=Plasmid+pBP136+from+Bordetella+pertussis+represents+an+ancestral+form+of+IncP-1beta+plasmids+without+accessory+mobile+elements.">Plasmid pBP136 from Bordetella pertussis represents an ancestral form of IncP-1beta plasmids without accessory mobile elements.</a> Microbiology. 152 (12), 3477-3484 (2006).</li><li>Simon, R., Priefer, U., P&#252;hler, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+broad+host+range+mobilization+system+for+in+vivo+genetic+engineering:+transposon+mutagenesis+in+gram+negative+bacteria.">A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in gram negative bacteria.</a> Nature Biotechnology. 1 (9), 784-791 (1983).</li><li>Andersen, J. 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=New+unstable+variants+of+green+fluorescent+protein+for+studies+of+transient+gene+expression+in+bacteria.">New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria.</a> Applied and Environmental Microbiology. 64 (6), 2240-2246 (1998).</li><li>Shintani, M., 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=Characterization+of+the+replication,+maintenance,+and+transfer+features+of+the+IncP-7+plasmid+pCAR1,+which+carries+genes+involved+in+carbazole+and+dioxin+degradation.">Characterization of the replication, maintenance, and transfer features of the IncP-7 plasmid pCAR1, which carries genes involved in carbazole and dioxin degradation.</a> Applied and Environmental Microbiology. 72 (5), 3206-3216 (2006).</li><li>Shintani, M., 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=Single-cell+analyses+revealed+transfer+ranges+of+IncP-1,+IncP-7,+and+IncP-9+plasmids+in+a+soil+bacterial+community.">Single-cell analyses revealed transfer ranges of IncP-1, IncP-7, and IncP-9 plasmids in a soil bacterial community.</a> Applied and Environmental Microbiology. 80 (1), 138-145 (2014).</li><li>Jarvis, B., Wilrich, C., Wilrich, P. 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N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transposon+vectors+containing+non-antibiotic+resistance+selection+markers+for+cloning+and+stable+chromosomal+insertion+of+foreign+genes+in+gram-negative+bacteria.">Transposon vectors containing non-antibiotic resistance selection markers for cloning and stable chromosomal insertion of foreign genes in gram-negative bacteria.</a> Journal of Bacteriology. 172 (11), 6557-6567 (1990).</li><li>Bagdasarian, M., 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=Specific-purpose+plasmid+cloning+vectors.+II.+Broad+host+range,+high+copy+number,+RSF1010-derived+vectors,+and+a+host-vector+system+for+gene+cloning+in+Pseudomonas.">Specific-purpose plasmid cloning vectors. II. Broad host range, high copy number, RSF1010-derived vectors, and a host-vector system for gene cloning in Pseudomonas.</a> Gene. 16 (1-3), 237-247 (1981).</li><li>Maeda, K., 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=Complete+nucleotide+sequence+of+carbazole/dioxin-degrading+plasmid+pCAR1+in+Pseudomonas+resinovorans+strain+CA10+indicates+its+mosaicity+and+the+presence+of+large+catabolic+transposon+Tn4676.">Complete nucleotide sequence of carbazole/dioxin-degrading plasmid pCAR1 in Pseudomonas resinovorans strain CA10 indicates its mosaicity and the presence of large catabolic transposon Tn4676.</a> Journal of Molecular Biology. 326 (1), 21-33 (2003).</li><li>Takahashi, Y., Shintani, M., Yamane, H., Nojiri, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+complete+nucleotide+sequence+of+pCAR2:+pCAR2+and+pCAR1+were+structurally+identical+IncP-7+carbazole+degradative+plasmids.">The complete nucleotide sequence of pCAR2: pCAR2 and pCAR1 were structurally identical IncP-7 carbazole degradative plasmids.</a> Bioscience, Biotechnology, and Biochemistry. 73 (3), 744-746 (2009).</li></ol>

Here, we present a high-resolution protocol for detecting differences in conjugation frequency under different conditions, using a MPN method to estimate the number of transconjugants. One important step in the protocol is diluting the mixture of donor and recipient after mating until no transconjugants grow. Another step is adding high concentrations of antibiotics to the selective liquid medium to prevent further conjugation. These procedures can reduce the background caused by further conjugation in the selective medi...

Bacterial conjugation of mobile genetic elements, conjugative plasmids, and integrative and conjugative elements (ICEs) is important for the horizontal spread of genetic information. It can promote rapid bacterial evolution and adaptation and transmit multidrug resistance genes1,2. The conjugation frequency can be affected by proteins encoded on the conjugative elements for mobilization of DNA (MOB) and mating pair formation (MPF), including sex pili, which are classified according to MOB and MPF type3,4,5. It can also be affected by the donor and recipient pair6 and the growth conditions of the cells7,8,9,10,11,12 (growth rate, cell density, solid surface or liquid medium, temperature, nutrient availability, and the presence of cations). To understand how the conjugative elements spread among bacteria, it is necessary to compare conjugation frequency in detail.
The conjugation frequency between donor and recipient pairs after mating are usually estimated by conventional methods as follows. (i) First, the numbers of donor and recipient colonies are counted; (ii) then, the recipient colonies, which received the conjugative elements (= transconjugants) are counted; (iii) and finally, the conjugation frequency is calculated by dividing the colony forming units (CFU) of the transconjugants by those of the donor and/or recipient13. However, when using this method, the background is high due to additional conjugation events that can also occur on the selective plates used to obtain transconjugants when the cell density is high10. Therefore, it is difficult to detect small differences in frequency (below a 10-fold difference). We recently introduced a most probable number (MPN) method using liquid medium containing a higher concentration of antibiotics. This method reduced the background by inhibiting further conjugation in selective medium; thus, the conjugation frequency could be estimated with higher resolution.
Conjugation can be divided into three steps: (1) attachment of the donor-recipient pair (2) initiation of conjugative transfer, and (3) dissociation of the pair14. During steps (1) and (3), there is physical interaction between the donor and recipient cells; thus, cell density and the environmental conditions can influence these steps, although the features of the sex pili are also important. Step (2) is likely regulated by the expression of several genes involved in conjugation in response to external changes, which could be affected by various features of the plasmid, donor, and recipient. Although the physical attachment or detachment of donor-recipient pairs can be mathematically simulated using an estimation of cells as particles, the frequency of step (2) should be experimentally measured. There have been a few reports on direct observations of how often donors can initiate conjugation [step (2)] using fluorescence microscopy15,16; however, these methods are not high-throughput because a large number of cells must be monitored. Therefore, we developed a new method to estimate the probability of the occurrence of step (2) by using fluorescence activated cell sorting (FACS). Our method can be applied to any plasmid, without identification of the essential genes for conjugation.

<table>
	<tbody>
		<tr>
			<td>MoFlo XDP</td>
			<td>Beckman-Coulter</td>
			<td>ML99030</td>
			<td>FACS</td>
		</tr>
		<tr>
			<td>IsoFlow</td>
			<td>Beckman-Coulter</td>
			<td>8599600</td>
			<td>Sheath solution</td>
		</tr>
		<tr>
			<td>Fluorospheres (10 &#956;m)</td>
			<td>Beckman-Coulter</td>
			<td>6605359</td>
			<td>beads to set up the FACS</td>
		</tr>
		<tr>
			<td>Incubator</td>
			<td>Yamato Scientific Co. Ltd</td>
			<td>211197-IC802</td>
			<td></td>
		</tr>
		<tr>
			<td>UV-VIS Spectrophotometer UV-1800</td>
			<td>SIMADZU Corporation</td>
			<td>UV-1800</td>
			<td></td>
		</tr>
		<tr>
			<td>96-well plates</td>
			<td>NIPPON Genetics Co, Ltd</td>
			<td>TR5003</td>
			<td></td>
		</tr>
		<tr>
			<td>microplate type Petri dish</td>
			<td>AXEL</td>
			<td>1-9668-01</td>
			<td>for validation of sorting</td>
		</tr>
		<tr>
			<td>membrane filter</td>
			<td>ADVANTEC</td>
			<td>C045A025A</td>
			<td>for filter mating</td>
		</tr>
		<tr>
			<td>pippettes</td>
			<td>Nichiryo CO. Ltd</td>
			<td>00-NPX2-20, 
			00-NPX2-200, 
			00-NPX2-1000</td>
			<td>0.5-10 &#956;L, 20-200 &#956;L, 100-1000 &#956;L</td>
		</tr>
		<tr>
			<td>multi-channel pippetes</td>
			<td>Nichiryo CO. Ltd</td>
			<td>00-NPM-8VP, 
			00-NPM-8LP</td>
			<td>0.5-10 &#956;L, 20-200 &#956;L</td>
		</tr>
		<tr>
			<td>Tryptone</td>
			<td>BD Difco</td>
			<td>211705</td>
			<td></td>
		</tr>
		<tr>
			<td>Yeast extract</td>
			<td>BD Difco</td>
			<td>212750</td>
			<td></td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>Sigma</td>
			<td>S-5886</td>
			<td></td>
		</tr>
		<tr>
			<td>Agar</td>
			<td>Nakarai tesque</td>
			<td>01162-15</td>
			<td></td>
		</tr>
		<tr>
			<td>rifampicin</td>
			<td>Wako</td>
			<td>185-01003</td>
			<td></td>
		</tr>
		<tr>
			<td>gentamicin</td>
			<td>Wako</td>
			<td>077-02974</td>
			<td></td>
		</tr>
		<tr>
			<td>kanamycin</td>
			<td>Wako</td>
			<td>115-00342</td>
			<td></td>
		</tr>
		<tr>
			<td>Petri dish</td>
			<td>AXEL</td>
			<td>3-1491-51</td>
			<td>JPND90-15</td>
		</tr>
		<tr>
			<td>microtubes</td>
			<td>Fukaekasei</td>
			<td>131-815C</td>
			<td></td>
		</tr>
		<tr>
			<td>500 mL disposable spinner flask</td>
			<td>Corning</td>
			<td>CLS3578</td>
			<td></td>
		</tr>
	</tbody>
</table>

high-resolution comparison of bacterial conjugation frequencies

Bacterial conjugation is an important step in the horizontal transfer of antibiotic resistance genes via a conjugative DNA element. In-depth comparisons of conjugation frequency under different conditions are required to understand how the conjugative element spreads in nature. However, conventional methods for comparing conjugation frequency are not appropriate for in-depth comparisons because of the high background caused by the occurrence of additional conjugation events on the selective plate. We successfully reduced the background by introducing a most probable number (MPN) method and a higher concentration of antibiotics to prevent further conjugation in selective liquid medium. In addition, we developed a protocol for estimating the probability of how often donor cells initiate conjugation by sorting single donor cells into recipient pools by fluorescence-activated cell sorting (FACS). Using two plasmids, pBP136 and pCAR1, the differences in conjugation frequency in Pseudomonas putida cells could be detected in liquid medium at different stirring rates. The frequencies of conjugation initiation were higher for pBP136 than for pCAR1. Using these results, we can better understand the conjugation features in these two plasmids.

Comparison of conjugation frequency by the MPN method
In our previous report, we compared the conjugation frequencies of pBP136::gfp and pCAR1::gfp in three-fold diluted LB (1/3 LB) liquid medium with different stirring rates after a 45 min mating using 125 mL spinner flasks10. We compared the conjugation frequencies of pBP136::gfp and pCAR1::gfp with 106 CFU/mL...

Watch this Scientific Journal Video about High-Resolution Comparison of Bacterial Conjugation Frequencies at JoVE.com

High-Resolution Comparison of Bacterial Conjugation Frequencies

With an aim to understand the behaviors of various bacterial conjugative DNA elements under different conditions, we describe a protocol for detecting differences in conjugation frequency, with high resolution, to estimate how efficiently the donor bacterium initiates conjugation.

Bacterial conjugation is an important step in the horizontal transfer of antibiotic resistance genes via a conjugative DNA element. In-depth comparisons ...

This method can help answer key questions in the microbiology field about how often plasmid DNA can be spread among different bacteria. The main advantage of this technique is that by reducing the background, we can detect small differences in the conjugation frequency with a high resolution. Demonstrating the procedure will be Kosuke Yanagiya, a graduate student from my laboratory.To calculate the conjugation frequency by most probable number, filter mate one milliliter from an overnight donor culture with one milliliter from an overnight recipient culture for 45 minutes at 30 degrees Celsius, as just demonstrated. While the co-culture is incubating, serially dilute the original donor and recipient cultures for plating in triplicate onto donor Luria broth, or LB, plus kanamycin, or recipient LB plus gentamycin plates for a two-day culture at 30 degrees Celsius. At the end of the incubation, resuspend the culture on the filter in sterile LB containing kanamycin and gentamycin for serial dilution in a 96-well cell culture plate in quadruplicate.After two days at 30 degrees Celsius, manually count the colony-forming units, or CFUs, on the donor and recipient agar plates and the number of wells in which the transconjugants grow by light microscopy. To calculate the most probable number and its deviation, open the MPN calculation program. Enter the name and date of the experiment, the number of the test series, and the maximum number of dilutions in row seven of the program sheet of the spreadsheet file.In the automatically-produced input data tables, enter the formula in the dilution factor D column, 0.01 in the volume in milliliters or GW column, and four in the number of tubes N column. Enter the number of wells in which the transconjugants grew at each sample dilution and click calculate results to obtain the results as most probable number per milliliter, and the upper and lower 95%confidence limits. Then divide the number of transconjugants by the number of donor and recipient colony forming units per milliliter to calculate the conjugation frequency of the plasmids.In this representative experiment, the conjugation frequency of both plasmids increased at higher stirring rates with a maximum difference in conjugation frequency observed between zero and 400 RPM for cultures introduced to the pBP136:gfp plasmid, and between zero and 200 RPM for cultures that were introduced to the pCAR1:gfp plasmid. To determine the density of recipient cells required to compare the probability of conjugation, mating assays were performed with different donor and recipient densities. In this representative experiment, pBP136:gfp transconjugants were detected in 100%of the wells containing one times 10 to the third CFU of donor and one times 10 to the fifth to one times 10 to the seventh CFU of recipient, and those with one times 10 to the second CFU of donor and one times 10 to the sixth to 10 to the seventh CFU of recipient, indicating that the cell density was too high.Mating assays with 10 CFU of donor and 10 to the sixth or 10 to the fifth CFU of recipient, however, resulted in a decreased number of transconjugant positive wells. Thus, 10 to the fifth CFU of recipient was predicted to be required for mating with a single donor cell. Mating assays with pCAR1:gfp at different densities of donor and recipient strains demonstrated similar findings, although overall the percentages of transconjugant positive wells were much lower than those of pBP136:gfp.Assuming that the donor and recipient cells can attach to each other similarly, the probability of conjugation initiation for the pCAR1 donor was lower than that for the pBP136 donor. Based on these results, it was estimated that 10 to the seventh CFU of recipient was required for a single donor cell sorted by FACS. After counting the numbers of transconjugant positive wells, the percentage of transconjugant positive wells for pBP136:gfp was determined to be larger than that for pCAR1:gfp, demonstrating a more than 36-fold difference in the probability of donor initiated conjugation between these two plasmids.While attempting the procedure, it's important to remember to always dilute the bacterial mixtures carefully.

high-resolution-comparison-of-bacterial-conjugation-frequencies

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Genetics

Conjugative Mating Assays for Sequence-specific Analysis of Transfer Proteins Involved in Bacterial Conjugation

The transfer of genetic material by bacterial conjugation is a process that takes place via complexes formed by specific transfer proteins. In Escherichia coli, these transfer proteins make up a DNA transfer machinery known as the mating pair formation, or DNA transfer complex, which facilitates conjugative plasmid transfer. The objective of this paper is to provide a method that can be used to determine the role of a specific transfer protein that is involved in conjugation using a series of deletions and/or point mutations in combination with mating assays. The target gene is knocked out on the conjugative plasmid and is then provided in trans through the use of a small recovery plasmid harboring the target gene. Mutations affecting the target gene on the recovery plasmid can reveal information about functional aspects of the target protein that result in the alteration of mating efficiency of donor cells harboring the mutated gene. Alterations in mating efficiency provide insight into the role and importance of the particular transfer protein, or a region therein, in facilitating conjugative DNA transfer. Coupling this mating assay with detailed three-dimensional structural studies will provide a comprehensive understanding of the function of the conjugative transfer protein as well as provide a means for identifying and characterizing regions of protein-protein interaction.

Here, we present a protocol to knockout a gene of interest involved in plasmid conjugation and subsequently analyze the impact of its absence using mating assays. The function of the gene is further explored to a specific region of its sequence using deletion or point mutations.

The transfer of genetic material by bacterial conjugation is a process that takes place via complexes formed by specific transfer proteins. In Escherichia ...

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 ...

High-resolution Melting PCR for Complement Receptor 1 Length Polymorphism Genotyping: An Innovative Tool for Alzheimer's Disease Gene Susceptibility Assessment

Complement receptor 1 (CR1), a transmembrane glycoprotein that plays a key role in the innate immune system, is expressed on many cell types, but especially on red blood cells (RBCs). As a receptor for the complement components C3b and C4b, CR1 regulates the activation of the complement cascade and promotes the phagocytosis of immune complexes and cellular debris, as well as the amyloid-beta (A&#946;) peptide in Alzheimer's disease (AD). Several studies have confirmed AD-associated single nucleotide polymorphisms (SNPs), as well as a copy-number variation (CNV) in the CR1 gene. Here, we describe an innovative method for determining the length polymorphism of the CR1 receptor. The receptor includes three domains, called long homologous repeats (LHR)-LHR-A, LHR-C, and LHR-D-and an n domain, LHR-B, where n is an integer between 0 and 3. Using a single pair of specific primers, the genetic material is used to amplify a first fragment of the LHR-B domain (the variant amplicon B) and a second fragment of the LHR-C domain (the invariant amplicon). The variant amplicon B and the invariant amplicon display differences at five nucleotides outside of the hybridization areas of said primers. The numbers of variant amplicons B and of invariant amplicons is deduced using a quantitative tool (high-resolution melting (HRM) curves), and the ratio of the variant amplicon B to the invariant amplicon differs according to the CR1 length polymorphism. This method provides several advantages over the canonical phenotype method, as it does not require fresh material and is cheaper, faster, and therefore applicable to larger populations. Thus, the use of this method should be helpful to better understand the role of CR1 isoforms in the pathogenesis of diseases such as AD.

Here, we describe an innovative method to determine complement receptor 1 (CR1) length polymorphisms for use in several applications, particularly the assessment of susceptibility to diseases such as Alzheimer&#39;s disease (AD). This method could be useful to better understand the role of CR1 isoforms in the pathogenesis of AD.

Complement receptor 1 (CR1), a transmembrane glycoprotein that plays a key role in the innate immune system, is expressed on many cell types, but ...

High Resolution Fluorescent In Situ Hybridization in Drosophila Embryos and Tissues Using Tyramide Signal Amplification

In our efforts to determine the patterns of expression and subcellular localization of Drosophila RNAs on a genome-wide basis, and in a variety of tissues, we have developed numerous modifications and improvements to our original fluorescent in situ hybridization (FISH) protocol. To facilitate throughput and cost effectiveness, all steps, from probe generation to signal detection, are performed using exon 96-well microtiter plates. Digoxygenin (DIG)-labelled antisense RNA probes are produced using either cDNA clones or genomic DNA as templates. After tissue fixation and permeabilization, probes are hybridized to transcripts of interest and then detected using a succession of anti-DIG antibody conjugated to biotin, streptavidin conjugated to horseradish peroxidase (HRP) and fluorescently conjugated tyramide, which in the presence of HRP, produces a highly reactive intermediate that binds to electron dense regions of immediately adjacent proteins. These amplification and localization steps produce a robust and highly localized signal that facilitates both cellular and subcellular transcript localization. The protocols provided have been optimized to produce highly specific signals in a variety of tissues and developmental stages. References are also provided for additional variations that allow the simultaneous detection of multiple transcripts, or transcripts and proteins, at the same time.

High Resolution Fluorescent In Situ Hybridization in Drosophila Embryos and Tissues Using Tyramide Signal Amplification

The described RNA in situ hybridization protocol allows the detection of RNA in whole Drosophila embryos or dissected tissues. Using 96-well microtiter plates and tyramide signal amplification, transcripts can be detected at high resolution, sensitivity, and throughput, and at a relatively low cost.

In our efforts to determine the patterns of expression and subcellular localization of Drosophila RNAs on a genome-wide basis, and in a variety of ...

Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions

The three-dimensional organization of the genome is linked to its function. For example, regulatory elements such as transcriptional enhancers control the spatio-temporal expression of their target genes through physical contact, often bridging considerable (in some cases hundreds of kilobases) genomic distances and bypassing nearby genes. The human genome harbors an estimated one million enhancers, the vast majority of which have unknown gene targets. Assigning distal regulatory regions to their target genes is thus crucial to understand gene expression control. We developed Promoter Capture Hi-C (PCHi-C) to enable the genome-wide detection of distal promoter-interacting regions (PIRs), for all promoters in a single experiment. In PCHi-C, highly complex Hi-C libraries are specifically enriched for promoter sequences through in-solution hybrid selection with thousands of biotinylated RNA baits complementary to the ends of all promoter-containing restriction fragments. The aim is to then pull-down promoter sequences and their frequent interaction partners such as enhancers and other potential regulatory elements. After high-throughput paired-end sequencing, a statistical test is applied to each promoter-ligated restriction fragment to identify significant PIRs at the restriction fragment level. We have used PCHi-C to generate an atlas of long-range promoter interactions in dozens of human and mouse cell types. These promoter interactome maps have contributed to a greater understanding of mammalian gene expression control by assigning putative regulatory regions to their target genes and revealing preferential spatial promoter-promoter interaction networks. This information also has high relevance to understanding human genetic disease and the identification of potential disease genes, by linking non-coding disease-associated sequence variants in or near control sequences to their target genes.

DNA regulatory elements, such as enhancers, control gene expression by physically contacting target gene promoters, often through long-range chromosomal interactions spanning large genomic distances. Promoter Capture Hi-C (PCHi-C) identifies significant interactions between promoters and distal regions, enabling the assignment of potential regulatory sequences to their target genes.

The three-dimensional organization of the genome is linked to its function. For example, regulatory elements such as transcriptional enhancers control the ...

Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere

The intimate interaction between plant host and associated microorganisms is crucial in determining plant fitness, and can foster improved tolerance to abiotic stresses and diseases. As the plant microbiome can be highly complex, low-cost, high-throughput methods such as amplicon-based sequencing of the 16S rRNA gene are often preferred for characterizing its microbial composition and diversity. However, the selection of appropriate methodology when conducting such experiments is critical for reducing biases that can make analysis and comparisons between samples and studies difficult. This protocol describes in detail a standardized methodology for the collection and extraction of DNA from soil, rhizosphere, and root samples. Additionally, we highlight a well-established 16S rRNA amplicon sequencing pipeline that allows for the exploration of the composition of bacterial communities in these samples, and can easily be adapted for other marker genes. This pipeline has been validated for a variety of plant species, including sorghum, maize, wheat, strawberry, and agave, and can help overcome issues associated with the contamination from plant organelles.

Here, we describe a protocol to obtain amplicon sequence data of soil, rhizosphere, and root endosphere microbiomes. This information can be used to investigate the composition and diversity of plant-associated microbial communities, and is suitable for the use with a wide range of plant species.

The intimate interaction between plant host and associated microorganisms is crucial in determining plant fitness, and can foster improved tolerance to ...

A Fluorescence-based Method to Study Bacterial Gene Regulation in Infected Tissues

Bacterial virulence genes are often regulated at the transcriptional level by multiple factors that respond to different environmental signals. Some factors act directly on virulence genes; others control pathogenesis by adjusting the expression of downstream regulators or the accumulation of signals that affect regulator activity. While regulation has been studied extensively during in vitro growth, relatively little is known about how gene expression is adjusted during infection. Such information is important when a particular gene product is a candidate for therapeutic intervention. Transcriptional approaches like quantitative, real-time RT-PCR and RNA-Seq are powerful ways to examine gene expression on a global level but suffer from many technical challenges including low abundance of bacterial RNA compared to host RNA, and sample degradation by RNases. Evaluating regulation using fluorescent reporters is relatively easy and can be multiplexed with fluorescent proteins with unique spectral properties. The method allows for single-cell, spatiotemporal analysis of gene expression in tissues that exhibit complex three-dimensional architecture and physiochemical gradients that affect bacterial regulatory networks. Such information is lost when data are averaged over the bulk population. Herein, we describe a method for quantifying gene expression in bacterial pathogens in situ. The method is based on simple tissue processing and direct observation of fluorescence from reporter proteins. We demonstrate the utility of this system by examining the expression of Staphylococcus aureus thermonuclease (nuc), whose gene product is required for immune evasion and full virulence ex vivo and in vivo. We show that nuc-gfp is strongly expressed in renal abscesses and reveal heterogeneous gene expression due in part to apparent spatial regulation of nuc promoter activity in abscesses fully engaged with the immune response. The method can be applied to any bacterium with a manipulatable genetic system and any infection model, providing valuable information for preclinical studies and drug development.

Described here is a method for analyzing bacterial gene expression in animal tissues at a cellular level. This method provides a resource for studying the phenotypic diversity occurring within a bacterial population in response to the tissue environment during an infection.

Bacterial virulence genes are often regulated at the transcriptional level by multiple factors that respond to different environmental signals. Some ...

Identifying Mutations by High Resolution Melting in a TILLING Population of Rice

Target Induced Local Lesions In Genomes (TILLING) is a strategy of reverse genetics for the high-throughput screening of induced mutations. However, the TILLING system has less applicability for insertion/deletion (Indel) detection and traditional TILLING needs more complex steps, like CEL I nuclease digestion and gel electrophoresis. To improve the throughput and selection efficiency, and to make the screening of both Indels and single base substitions (SBSs) possible, a new high-resolution melting (HRM)-based TILLING system is developed. Here, we present a detailed HRM-TILLING protocol and show its application in mutation screening. This method can analyze the mutations of PCR amplicons by measuring the denaturation of double-stranded DNA at high temperatures. HRM analysis is directly performed post-PCR without additional processing. Moreover, a simple, safe and fast (SSF) DNA extraction method is integrated with HRM-TILLING to identify both Indels and SBSs. Its simplicity, robustness and high throughput make it potentially useful for mutation scanning in rice and other crops.

In this article, we present the protocol that is described as high-resolution melting analysis (HRM)-based Target Induced Local Lesions In Genomes (TILLING). This method utilizes fluorescence changes during the melting of the DNA duplex and is suitable for high-throughput screening of both insertion/deletion (Indel) and single base substition (SBS).

Target Induced Local Lesions In Genomes (TILLING) is a strategy of reverse genetics for the high-throughput screening of induced mutations. However, the ...

Tomato Root Transformation Followed by Inoculation with Ralstonia Solanacearum for Straightforward Genetic Analysis of Bacterial Wilt Disease

Ralstonia solanacearum is a devastating soil borne vascular pathogen that can infect a large range of plant species, causing an important threat to agriculture. However, the Ralstonia model is considerably underexplored in comparison to other models involving bacterial plant pathogens, such as Pseudomonas syringae in Arabidopsis. Research targeted to understanding the interaction between Ralstonia and crop plants is essential to develop sustainable solutions to fight against bacterial wilt disease but is currently hindered by the lack of straightforward experimental assays to characterize the different components of the interaction in native host plants. In this scenario, we have developed a method to perform genetic analysis of Ralstonia infection of tomato, a natural host of Ralstonia. This method is based on Agrobacterium rhizogenes-mediated transformation of tomato roots, followed by Ralstonia soil-drenching inoculation of the resulting plants, containing transformed roots expressing the construct of interest. The versatility of the root transformation assay allows performing either gene overexpression or gene silencing mediated by RNAi. As a proof of concept, we used this method to show that RNAi-mediated silencing of SlCESA6 in tomato roots conferred resistance to Ralstonia. Here, we describe this method in detail, enabling genetic approaches to understand bacterial wilt disease in a relatively short time and with small requirements of equipment and plant growth space.

Tomato Root Transformation Followed by Inoculation with Ralstonia Solanacearum for Straightforward Genetic Analysis of Bacterial Wilt Disease

Here, we present a versatile method for tomato root transformation followed by inoculation with Ralstonia solanacearum to perform straightforward genetic analysis for the study of bacterial wilt disease.

Ralstonia solanacearum is a devastating soil borne vascular pathogen that can infect a large range of plant species, causing an important threat to ...

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 ...