Name: field-deployable candidatus liberibacter asiaticus detection using recombinase polymerase amplification combined with crispr-cas12a
Uploaded: 2022-12-23T12:45:00
Description: Watch this Scientific Journal Video about Field-Deployable Candidatus Liberibacter asiaticus Detection Using Recombinase Polymerase Amplification Combined with CRISPR-Cas12a at JoVE.com

This work was financially supported by the National Key R &#38; D Program of China (2021YFD1400805), the Major Science and Technology R &#38; D Program of Jiangxi Province (20194ABC28007), Projects of Jiangxi Education Department (GJJ201449), and the Collaborative Innovation of Modern Agricultural Scientific Research in Jiangxi Province (JXXTCX2015002(3+2)-003).

1. Construction of the CLas-DETECTR
NOTE: The construction of CLas-DETECTR is a four-step process: solution preparation, citrus total DNA isolation, isothermal DNA amplification, and result visualization. The schematic of the CLas-DETECTR assay is illustrated in Figure 1A.
<ol>
	<li>Solution preparation
	<ol>
		<li>Prepare buffer A: 20 mM NaOH in 6% PEG 200. For 100 mL, add 113 mg of NaOH and 6 g of PEG 200 into 80 mL of H2O in a bottle. Incubate the ...

<ol>
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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=Development+of+a+recombinase+polymerase+based+isothermal+amplification+combined+with+lateral+flow+assay+(HLB-RPA-LFA)+for+rapid+detection+of+&amp;#34;Candidatus+Liberibacter+asiaticus&amp;#34;.">Development of a recombinase polymerase based isothermal amplification combined with lateral flow assay (HLB-RPA-LFA) for rapid detection of &amp;#34;Candidatus Liberibacter asiaticus&amp;#34;.</a> PLoS One. 13 (12), e0208530 (2018).</li><li>Ravindran, A., Levy, J., Pierson, E., Gross, D. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Development+of+a+loop-mediated+isothermal+amplification+procedure+as+a+sensitive+and+rapid+method+for+detection+of+'Candidatus+Liberibacter+solanacearum'+in+potatoes+and+psyllids.">Development of a loop-mediated isothermal amplification procedure as a sensitive and rapid method for detection of 'Candidatus Liberibacter solanacearum' in potatoes and psyllids.</a> Phytopathology. 102 (9), 899-907 (2012).</li><li>Chertow, D. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Next-generation+diagnostics+with+CRISPR.">Next-generation diagnostics with CRISPR.</a> Science. 360 (6387), 381-382 (2018).</li><li>Chen, J. 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C., 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=Diagnostics+of+infections+produced+by+the+plant+viruses+TMV,+TEV,+and+PVX+with+CRISPR-Cas12+and+CRISPR-Cas13.">Diagnostics of infections produced by the plant viruses TMV, TEV, and PVX with CRISPR-Cas12 and CRISPR-Cas13.</a> ACS Synthetic Biology. 11 (7), 2384-2393 (2022).</li><li>Lu, X., 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+rapid,+equipment-free+method+for+detecting+Phytophthora+infestans+in+the+field+using+a+lateral+flow+strip-based+recombinase+polymerase+amplification+assay.">A rapid, equipment-free method for detecting Phytophthora infestans in the field using a lateral flow strip-based recombinase polymerase amplification assay.</a> Plant Disease. 104 (11), 2774-2778 (2020).</li><li>Lobato, I. M., O'Sullivan, C. 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This study presents a rapid and portable method to detect CLas named CLas-DETECTR, which combines the RPA and CRISPR-Cas12a systems. The workflow is illustrated in Figure 1. CLas-DETECTR detects CLas with specificity and sensitivity (Figure 2 and Figure 3). Furthermore, using Newhall leaf samples, CLas-DETECTR detects CLas with the same sensitivity as qPCR (Figure 4). Notably, the detec...

Huanglongbing (HLB) is one of the most problematic citrus diseases worldwide1. HLB is caused by the phloem-colonizing and fastidious bacteria Candidatus Liberibacter spp., including Candidatus Liberibacter asiaticus (CLas), Ca. L. africanus, and Ca. L. americanus2. The most prevalent HLB-associated species in China and the USA is CLas, which is transmitted by Asian citrus psyllids (Diaphorina citri) or through grafting3. After being infected by CLas, citrus trees demonstrate growth decline until death2. The common symptoms of citrus leaves infected with CLas are blotchy mottle, green islands (small circular dark green dots), raised corky veins on thicker and leathery leaves, and nonuniform yellowing shoots2. In addition, fruits infected with CLas appear small and lopsided2.
Since no citrus variety is resistant to HLB and there is no therapeutic cure for HLB, the prevention of HLB requires the quarantine and isolation of CLas-positive citrus trees2,3. Therefore, early detection is critical for monitoring and quarantine to prevent the spread of CLas and minimize economic losses3. In addition, sensitive CLas detection is needed due to the low titer of CLas in plants during the early stage of infection3. In China, CLas detection is usually conducted by certain certified test centers. However, the detection process usually takes at least 1 week, and the detection fee is expensive.&#160;Therefore, to help monitor the HLB incidence
Various technologies have been applied to diagnose HLB4,5,6,7,8,9. Polymerase chain reaction (PCR) and quantitative PCR (qPCR) are the most used tools for CLas detection due to their high sensitivity and specificity4,5. However, those technologies rely heavily on expensive instruments and highly skilled personnel. In addition, several isothermal amplification methods, such as loop-mediated isothermal amplification (LAMP), have been developed as attractive alternatives to conventional PCR methods due to their simplicity, rapidity, and low cost8,9,10. However, it is challenging to apply them to accurately detect CLas due to the non-specific amplification signals, which may cause false-positive results.
RNA-guided CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated) endonuclease-based nucleic acid detection has been developed as a next-generation molecular diagnostics technology owing to its high sensitivity, specificity, and reliability11,12,13,14. These CRISPR/Cas diagnostics technologies rely on the collateral nuclease activity of Cas proteins to cleave single-stranded DNA (ssDNA) modified with a fluorescent reporter and a fluorescence quencher at each end of the oligonucleotides, as well as a fluorescence detection device to capture the released fluorescent reporter11,12. The nuclease activity of several Cas effectors activated by the CRISPR RNA (crRNA) target duplex can indiscriminately cleave the surrounding non-target ssDNA11. CRISPR-Cas12a (also called Cpf 1), a class 2 type V-A CRISPR/Cas system, demonstrates several advantages compared with Cas9, such as a lower mismatch tolerance and greater specificity13.&#160;The Cas12a/crRNA system has been applied for the sensitive and specific detection of the nucleic acids of human pathogens and phytopathogens14,15,16,17,18. Therefore, utilizing the Cas12a/crRNA system should enable the accurate and sensitive detection of the nucleic acid of CLas.
Cas12a alone is not theoretically sensitive enough to detect low levels of nucleic acids. Therefore, to improve its detection sensitivity, CRISPR-Cas12a detection is typically combined with an isothermal amplification step14,15. Recombinase polymerase amplification (RPA) enables sensitive and rapid isothermal DNA amplification in a temperature range from 37 &#176;C to 42 &#176;C19.
A detection platform called DETECTR (DNA Endonuclease Targeted CRISPR Trans Reporter) that combines the DNase activity of Cas12a with RPA and a fluorescence readout has been recently devised12 and has been shown to detect nucleic acid with higher sensitivity20. Furthermore, the fluorescence signal emitted from the positive samples can be observed through a handheld fluorescence detection device in the field.
Since we amplified DNA with RPA, designed crRNA targeting the five-copy nrdB (ribonucleotide reductase &#946;- subunit) gene specific to CLas21, and employed the DNase activity of the Cas12a protein, we called this CLas detection method CLas-DETECTR. Compared with existing CLas detection methods, CLas-DETECTR is fast, accurate, sensitive, and deployable.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>AxyPrep DNA Gel Extraction Kit</td>
			<td>Corning</td>
			<td>09319KE1</td>
			<td>China</td>
			<td></td>
		</tr>
		<tr>
			<td>Bacterial Genomic DNA Extraction Kit</td>
			<td>Solarbio</td>
			<td>D1600</td>
			<td>China</td>
			<td></td>
		</tr>
		<tr>
			<td>EnGen LbCas12a&#160;</td>
			<td>TOLOBIO</td>
			<td>32104-01</td>
			<td>China</td>
			<td></td>
		</tr>
		<tr>
			<td>Ex Taq Version 2.0 plus dye</td>
			<td>TaKaRa</td>
			<td>RR902A</td>
			<td>China</td>
			<td></td>
		</tr>
		<tr>
			<td>Handheld fluorescent detection device&#160;</td>
			<td>LUYOR</td>
			<td>3415RG</td>
			<td>China</td>
			<td></td>
		</tr>
		<tr>
			<td>Hole puncher&#160;</td>
			<td>Deli</td>
			<td>114</td>
			<td>China</td>
			<td></td>
		</tr>
		<tr>
			<td>Magnesium acetate, MgOAc</td>
			<td>TwistDx</td>
			<td>TABAS03KIT</td>
			<td>UK</td>
			<td></td>
		</tr>
		<tr>
			<td>NaOH</td>
			<td>SCR</td>
			<td>10019718</td>
			<td>China</td>
			<td></td>
		</tr>
		<tr>
			<td>NEB buffer 3.1&#160;</td>
			<td>NEB</td>
			<td>B7203</td>
			<td>USA</td>
			<td></td>
		</tr>
		<tr>
			<td>PCR strip tubes</td>
			<td>LABSELECT</td>
			<td>PST-0208-FT-C</td>
			<td>China</td>
			<td></td>
		</tr>
		<tr>
			<td>PEG 200&#160;</td>
			<td>Sigma</td>
			<td>P3015</td>
			<td>USA</td>
			<td></td>
		</tr>
		<tr>
			<td>PrimeSTAR Max DNA Polymeras</td>
			<td>TaKaRa</td>
			<td>R045A</td>
			<td>China</td>
			<td></td>
		</tr>
		<tr>
			<td>Quick-Load Purple 1 kb Plus DNA Ladder&#160;</td>
			<td>New England Biolabs</td>
			<td>N0550S</td>
			<td>USA</td>
			<td></td>
		</tr>
		<tr>
			<td>TB Green Premix Ex Taq II (Tli RNaseH Plus)</td>
			<td>TaKaRa</td>
			<td>RR820B</td>
			<td>China</td>
			<td></td>
		</tr>
		<tr>
			<td>TwistAmp Basic</td>
			<td>TwistDx</td>
			<td>TABAS03KIT</td>
			<td>UK</td>
			<td></td>
		</tr>
	</tbody>
</table>

field-deployable candidatus liberibacter asiaticus detection using recombinase polymerase amplification combined with crispr-cas12a

The early detection of Candidatus Liberibacter asiaticus (CLas) by citrus growers facilitates early intervention and prevents the spread of disease. A simple method for rapid and portable Huanglongbing (HLB) diagnosis is presented here that combines recombinase polymerase amplification and a fluorescent reporter utilizing the nuclease activity of the clustered regularly interspaced short palindromic repeats/CRISPR-associated 12a (CRISPR-Cas12a) system. The sensitivity of this technique is much higher than PCR. Furthermore, this method showed similar results to qPCR when leaf samples were used. Compared with conventional CLas detection methods, the detection method presented here can be completed in 90 min and works in an isothermal condition that does not require the use of PCR machines. In addition, the results can be visualized through a handheld fluorescent detection device in the field.

Here, we have described a portable platform, CLas-DETECTR, combing the RPA and CRISPR-Cas12a systems to diagnose HLB in the field. The schema of CLas-DETECTR is illustrated in Figure 1A.
When leaf samples from the HLB-infected and HLB-uninfected Newhall trees (Figure 1B), for which the presence of CLas was confirmed by PCR (Figure 1C), were subjected to the CLas-DETECTR test, a green fluorescence signal w...

Watch this Scientific Journal Video about Field-Deployable Candidatus Liberibacter asiaticus Detection Using Recombinase Polymerase Amplification Combined with CRISPR-Cas12a at JoVE.com

Field-Deployable Candidatus Liberibacter asiaticus Detection Using Recombinase Polymerase Amplification Combined with CRISPR-Cas12a

In this work, a rapid, sensitive, and portable detection method for Candidatus Liberibacter asiaticus based on recombinase polymerase amplification combined with CRISPR-Cas12a was developed.

Field-Deployable Candidatus Liberibacter asiaticus Detection Using Recombinase Polymerase Amplification Combined with CRISPR-Cas12a

The early detection of Candidatus Liberibacter asiaticus (CLas) by citrus growers facilitates early intervention and prevents the spread of disease. A ...

Huang long bing, abbreviated as HLB. It's a devastating citrus disease worldwide. In the most citrus-producing countries, such as China and the USA, HLB is caused by the phloem-restricted bacteria Candidatus Liberibacter asiaticus, abbreviated as CLas.Early detection of CLas were important for growers facilitating early intervention and preventing disease spread. So here we developed a new method for the rapid and portable HLB diagnosis, combining with the recombinase polymerase amplification and CRISPR-Cas12a system. We called it CLas-DETECTR.The sensitivity of our platform is much higher than PCR. Furthermore, it shows similar result with qPCR when the leaf samples was used. Compare with the conventional CLas detections, our method can be finished in 90 minutes, and works in an isothermal condition.The result also can be visualized through a handheld fluorescent detection device in the field. The CLas-DETECTR contains four steps:solution preparation, citrus total DNA isolation, isothermal DNA amplification, and the results of visualization. The schematic of the CLas-DETECTR assay is illustrated here.Buffer A, Solution B, and Solution C are prepared as described in the protocol. To save time and make this method suitable for field CLas detection, the E.coli polyethylene glycol-based approach were used to obtain crude plant extracts for DNA amplification. Citrus leaves are used in the tool.Punch the few pieces of leaf discs from leaf. Put leaf discs into a 1.5 milliliter Eppendorf tube. Then, add 200 microliter of Buffer A into the tube.Grind the leaf discs until smooth with a plastic rod manually. Leave the tube undisturbed for 10 minutes. The supernatant is subsequently applied to DNA amplification.For isothermal DNA amplification, add one microliter of supernatant from step 2.3 and one microliter of magnesium acetate into Solution B and mix well. In the lab, incubate them in a simple incubator at 37 degree for 15 minutes. To visualize the results, add 10 microliter of the mixture from step 3.2 into Solution C and mix well.Incubate them in the 37 degree incubator for 60 minutes. Wear a goggle, and observe the green fluorescence signal through a handheld fluorescent detection device. To test the specificity of CLas-DETECTR, first pure colonies of Agrobacterium tumefaciens GV3101, Xanthomonas citri subsp.citri which is the pathogen of the citrus canker and Burkholderia stabilis strain 1440 isolated in our lab were used to extract their genomic DNA. Then this three bacteria genomic DNA and the CLas-positive Newhall leaves genomic DNA were subjected to the CLas-DETECTR test. To test the sensitivity of CLas-DETECTR, a series of CLas DNA fragment dilutions were detected using PCR, CLas-DETECTR, and qPCR as described in the protocol After the specificity and the sensitivity test, the CLas-DETECTR method was used to detect the presence of the CLas in field.Leaf samples collected from Newhall sweet orange tree grown in the germplasm resource nursery on the campus of the Gannan Normal University, Jiangxi, China. qPCR, a convincing CLas detection method usually used in the lab was also applied. The leaf samples from HLB-infected and HLB-uninfected Newhall tree, in which the presence of the CLas was confirmed in our lab, were subjected to the CLas-DETECTR test.The green fluorescence signal was captured in the HLB-infected sample, but not in the HLB-uninfected and negative control. We determined the specificity of CLas-DETECTR using nucleic acids extracted from other bacteria. In the CLas-DETECTR assay, only gDNA extracted from CLas-positive Newhall leaves demonstrated green fluorescent signals.gDNA extracted from Agrobacterium tumefaciens GV3101, Xanthomonas citri subsp. citri and Burkholderia stabilis strain 1440 did not, which means the CLas-DETECTR can detect CLas specifically. We also tested the sensitivity of CLas-DETECTR using a series of CLas DNA dilutions, listed in the protocol.PCR can detect 201 copies per megaliter. On the other hand, CLas-DETECTR can detect 2.01 copies per megaliter, suggesting its availability as a sensitive field diagnostic. qPCR can detect 0.201 copies per megaliter and the Ct value is higher than 36.So CLas-DETECTR is two orders of magnitude more sensitive than traditional PCR and one order of a magnitude less sensitive than qPCR when diluted CLas specific amplicons was used. Finally, reexamined the feasibility of the CLas-DETECTR for field samples, and compared its sensitivity with qPCR. In figures, we see.We can see that the Ct value is higher than 36 when the CLas concentration is less than 0.2 copies per megaliter, which is a very low concentration. Among the 15 samples, the Ct value of the samples 1, 2, 3, 4, 8, 10, 13 and 14 detected by qPCR was less than 36. An apparent green fluorescence signals was observed.On the other hand, when the Ct value of the samples 6, 7, 9, 12, and 15 detected by qPCR was undetermined, no green fluorescent signals was observed. In addition, weak green fluorescent signals was observed when the CT value of sample 5 and 11 detected by qPCR was higher than 36. The results will suggest that our platform is a rapid, robust and sensitive tool for HLB diagnosis in the field.

Research

JoVE Journal

Biology

Principles of Site-Specific Recombinase (SSR) Technology

Principles of Site-Specific Recombinase SSR Technology

Site-specific recombinase (SSR) technology allows the manipulation of gene structure to explore gene function and has become an integral tool of molecular ...

Molecular Evolution of the Tre Recombinase

Here we report the generation of Tre recombinase through directed, molecular evolution. Tre recombinase recognizes a pre-defined target sequence within ...

Interview: HIV-1 Proviral DNA Excision Using an Evolved Recombinase

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Chromosome Replicating Timing Combined with Fluorescent In situ Hybridization

Chromosome Replicating Timing Combined with Fluorescent In situ Hybridization

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Rapid and Efficient Zebrafish Genotyping Using PCR with High-resolution Melt Analysis

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RNA Isolation from Cell Specific Subpopulations Using Laser-capture Microdissection Combined with Rapid Immunolabeling

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Development of a Quantitative Recombinase Polymerase Amplification Assay with an Internal Positive Control

It was recently demonstrated that recombinase polymerase amplification (RPA), an isothermal amplification platform for pathogen detection, may be used to ...

Isolation of Specific Genomic Regions and Identification of Associated Molecules by enChIP

The identification of molecules associated with specific genomic regions of interest is required to understand the mechanisms of regulation of the ...

Application of Passive Head Motion to Generate Defined Accelerations at the Heads of Rodents

Exercise is widely recognized as effective for various diseases and physical disorders, including those related to brain dysfunction. However, molecular ...

Using Colorimetric and RT-LAMP Analysis to Detect SARS-CoV-2 

Detecting SARS-CoV-2 Virus by Reverse Transcription-Loop-Mediated Isothermal Amplification

Author Spotlight: Advancing Pathogen Diagnostics with Standardized LAMP

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has dramatically impacted human health. It continues to be a threat to modern ...