Name: A Non-Coding Small RNA MicC Contributes to Virulence in Outer Membrane Proteins in Salmonella Enteritidis (Video) | JoVE Journal
Uploaded: 2021-01-27T14:00:00.000+00:00
Duration: 6 min 30 s
Description: Learn to create micC deletion mutants in Salmonella Enteritidis using λ-Red-mediated recombination. This protocol enables efficient gene inactivation for studying bacterial virulence and vaccine development.

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5 minutes

This study was supported by grants from the Chinese National Science Foundation (Nos. 31972651 and 31101826), Jiangsu High Education Science Foundation (No.14KJB230002), State Key Laboratory of Veterinary Biotechnology (No.SKLVBF201509), Nature Science Foundation Grant of Yangzhou (No.YZ2014019), A Project Funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).

All the experiments were conducted in accordance with the Guide for the Care and Use of Laboratory Animals of the National Research Council. The animal care and use committee of Yangzhou University approved all experiments and procedures applied on the animals (SYXK2016-0020).
1. Bacterial strains, plasmids, and culture conditions
<ol>
	<li>Use the bacteria and plasmids listed in Table 1.</li>
	<li>Culture bacteria in LB broth or on LB agar plates at 37 &#176;C, in the presence of 50 &#181;g/mL ampicillin (Amp) when appropriate.</li>
	<li>Culture strains containing temperature sensitive plasmids are used for deletion mutant construction at 30 &#176;C.</li>
</ol>
2. Clone micC gene of S. Enteritidis strain 50336
<ol>
	<li>Based on the upstream and downstream sequence of micC gene of S. Typhimurium strain SL1344, design primers vmicC-F and vmicC-R to amplify a fragment containing micC gene by PCR using SE50336 genomic DNA as template.</li>
	<li>Mix 5 &#181;L of 10x PCR reaction buffer, 2 &#181;L of dNTP mixture (2.5 mM), 1 &#181;L of vmicC-F and vmicC-R primers, respectively, 5 &#181;L of template, 1 &#181;L of Taq DNA polymerase and 35 &#181;L of ddH2O together for PCR.</li>
	<li>Use the following PCR reaction conditions:pre-denaturation at 94 &#730;C for 4 min; 94 &#730;C for 30 s, 53 &#730;C for 1 min, 72 &#730;C for 1 min for 25 cycles, and extension at 72 &#730;C for 10 min.</li>
	<li>Sequence the PCR product to obtain the micC gene sequence.</li>
</ol>
3. Construction of the micC deletion mutant
NOTE: The micC-negative mutant of Salmonella Enteritidis strain 50336 was constructed using &#955;-Red-mediated recombination as described previously13,14. The primers used are listed in Table 2.
<ol>
	<li>Amplify chloramphenicol cassette containing homology fragments of micC gene.
	<ol>
		<li>Design micC-F and micC-R primers to amplify the chloramphenicol (Cm) cassette from plasmid pKD3, including 50 bp homology extensions from the 5&#39; and 3&#39; of the micC gene.</li>
		<li>Extract the pKD3 plasmid as the PCR template.</li>
		<li>Mix 5 &#181;L of 10x PCR reaction buffer, 2 &#181;L of dNTP Mixture (2.5 mM), 1 &#181;L of micC-F and micC-R primers, respectively, 5 &#181;L of template, 1 &#181;L of Taq DNA polymerase and 35 &#181;L of ddH2O together as PCR reaction mixture</li>
		<li>Amplify the Cm cassette with the following PCR reaction conditions: pre-denaturation at 94 &#176;C for 4 min; 94 &#176;C for 1 min, 52 &#176;C for 1 min, 72 &#176;C for 1 min for 10 cycles; 94 &#176;C for 1 min, 63 &#176;C for 1 min, 72 &#176;C for 1 min for 25 cycles, and extension at 72 &#176;C for 10 min.</li>
		<li>Detect the size of PCR product by agarose gel electrophoresis. Purify and recover PCR product with DNA gel recovery kit, and determine the concentration of DNA by spectrophotometer. 
		CAUTION: PCR must be carried out twice. The first PCR product was diluted at a ratio of 1:200 and used as a template for the secondary PCR, to eliminate the interference of further recombination by pKD3 plasmid.</li>
	</ol>
	</li>
	<li>Construct 1st recombinant strain 50336&#916;micC::cat
	<ol>
		<li>Mix 100 &#181;L of SE50336 competent cells with 5 &#181;L of pKD46 plasmid uniformly and incubate on ice for 30 min. Heat shock the above mixture at 42 &#176;C for 90 s, and rapidly transfer the mixture to ice for 2 min to transform the pKD46 plasmid to SE50336. Screen positive colonies by culturing overnight at 30 &#176;C on an Amp (50 &#181;g/mL) resistant plate.</li>
		<li>Add 30 mM L-arabinose to SE50336/pKD46 liquid culture, and induce recombinase expression by a 30 &#176;C shaking culture for 1 h. Then prepare competent cells.</li>
		<li>Mix 100 ng of purified PCR product (step 3.1) and 40 &#181;L of SE50336/pKD46 competent cells into an electric shock cup (e.g., Bio-Rad). Carry out electric shock transformation with the parameters of voltage 1.8 kV, pulse 25 &#181;F and resistance 200 &#937;.</li>
		<li>After electrotransformation, transfer the mixture to 1 mL of SOC medium and a shaking culture at 150 rpm and 30 &#176;C for 1 h. Then smear the mixture on a Cm (34 &#181;g/mL) resistant LB plate and culture at 37 &#176;C overnight to screen positive colony.</li>
		<li>Culture the above positive colony at 42 &#176;C for 2 h. Screen the colony that is sensitive to Amp (50 &#181;g/mL) but resistant to Cm (34 &#181;g/mL) at 37 &#730;C overnight to obtain the 1st recombinant strain without pKD46.</li>
	</ol>
	</li>
	<li>Identify the 1st recombinant strain 50336&#916;micC::Cat.
	<ol>
		<li>Extract 50336&#916;micC::Cat genomic DNA as the PCR template. Use the same PCR reaction components as in step 2.1. Carry out the PCR reaction with the same conditions as in step 2.1.</li>
		<li>Detect the size of PCR product by agarose gel electrophoresis and sequence the PCR product.</li>
	</ol>
	</li>
	<li>Construct deletion mutant 50336&#916;micC.
	<ol>
		<li>Electroporate 100 ng of plasmid pCP20 into 40 &#181;L of 50336&#916;micC::Cat competent cells with the parameters of voltage 1.8 kV, pulse 25 &#181;F and resistance 200 &#937;, screen positive transformants on both Amp (50 &#181;g/mL) and Cm (34 &#181;g/mL) resistant plate at 30 &#176;C.</li>
		<li>Transfer above positive transformants into non-resistant LB and culture them overnight at 42 &#176;C, and then isolate single colonies on an LB plate at 37 &#176;C. Select the colony that is sensitive to both Amp and Cm. This mutant is the micC deletion mutant SE50336&#916;micC.</li>
		<li>Verify 50336&#916;micC by PCR.
		<ol>
			<li>Extract 50336&#916;micC genomic DNA as PCR template. Mix 5 &#181;Lof 10x PCR reaction buffer, 2 &#181;L of dNTP Mixture (2.5 mM), 1 &#181;L of primer vmicC-F, 1 &#181;L of primer vmicC-R, 5 &#181;L of template, 1 &#181;L of Taq DNA polymerase and 35 &#181;L of ddH2O together for PCR.</li>
			<li>Use the following PCR reaction conditions:pre-denaturation at 94 &#176;C for 4 min; 94 &#176;C for 30 s, 53 &#176;C for 1 min, 72 &#730;C for 1 min for 25 cycles, and extension at 72 &#176;C for 10min.</li>
		</ol>
		</li>
	</ol>
	</li>
</ol>
4. Construction of the micC complemented strain
<ol>
	<li>Design primers pBR-micC-F and pBR-micC-R with NheI and SalI restriction sites.
	<ol>
		<li>Amplify full-length micC gene with flank sequences using PCR reaction mixture that contains 5 &#181;L of SE50336 genomic DNA as template, primers 1 &#181;L of pBR-micC-F and 1 &#181;L of pBR-micC-R as primers, 5 &#181;Lof 10x PCR reaction buffer, 2 &#181;L of dNTP Mixture (2.5 mM), 2 &#181;L of dNTP Mixture (2.5 mM) and 35 &#181;L of ddH2O.</li>
		<li>Use the following PCR reaction conditions: pre-denaturation at 94 &#176;C for 4 min; 94 &#176;C for 30 s, 52 &#176;C for 50 s, 72 &#176;C for 1 min for 25 cycles, and extension at 72 &#176;C for 10 min. Purify and recover PCR product.</li>
	</ol>
	</li>
	<li>Digest PCR product and plasmid pBR322 respectively using restriction enzyme NheI and SalI, and ligate them using T4 ligase at 16 &#176;C overnight to obtain the plasmid pBR322-micC.</li>
	<li>Transform pBR322-micC into the SE50336&#916;micC competent cells, and screen positive transformant to obtain the complemented strain SE50336&#916;micC/pmicC. Extract plasmid pBR322-micC from complemented strain and verify it by restriction enzyme digestion and sequencing.</li>
</ol>
5. RNA isolation and quantitative real-time PCR
<ol>
	<li>Culture SE50336, 50336&#916;micC, and 50336&#916;micC/pmicC in LB medium overnight at 24 &#176;C with 180 rpm shake cultivation to an OD600 of 2.0. Collect bacterial culture by centrifugation at 13000 rpm for 2 min.</li>
	<li>Extract total RNA using TRIzol reagent. Incubate 50 &#181;L of isolated RNA with 2 &#181;L of DNaseI and 6 &#181;L of 10x buffer at 37 &#176;C for 30 min to remove DNA. Determine RNA quantity by pipetting 1 &#181;L of RNA sample to a micro-spectrophotometer.</li>
	<li>Synthesis of cDNA
	<ol>
		<li>Use 1 &#181;g of total RNA for cDNA synthesis in 20 &#181;L of reverse transcription reaction system (4 &#181;L of 5x buffer, 1 &#181;L of RT Enzyme mix, 1 &#181;L of RT primer mix, 10 &#181;L of total RNA, and 4 &#181;L of ddH2O). Incubate above reaction system at 37 &#176;C for 15 min and then at 85 &#176;C for 5 s.</li>
	</ol>
	</li>
	<li>Design primers based on the sequence of target genes ompA, ompC and ompD. Perform reverse transcription-PCR using a RT reagent kit. The PCR reaction components contain 2.5 &#181;Lof 10x PCR reaction buffer, 1 &#181;L of dNTP mixture (2.5 mM), 1 &#181;L of target gene (ompA, ompC or ompD) primers, 2.5 &#181;L of template, 0.5 &#181;L of Taq DNA polymerase and 17.5 &#181;L of ddH2O.
	<ol>
		<li>Use the following PCR reaction conditions:pre-denaturation at 94 &#176;C for 4 min; 94 &#176;C for 30 s, 60 &#176;C for 1 min, 72 &#176;C for 1 min for 25 cycles, and extension at 72 &#176;C for 10min.</li>
	</ol>
	</li>
	<li>Carry out real-time PCR using SYBR green RT-PCR kit in a RT-PCT instrument in triplicates.
	<ol>
		<li>Use the following PCR reaction components: 10 &#181;L of 2x SYBR buffer, 0.4 &#181;Lof forward primer and reverse primer respectively, 0.4 &#181;L of RoxDye II, 2 &#181;Lof cDNA and 6.8 &#181;L of RNase free H2O.</li>
		<li>Use the following PCR reaction conditions:pre-denaturation at 95 &#176;C for 1 min for one cycle; 95 &#176;C for 5 s, 60 &#176;C for 34 s for 40 cycles.</li>
		<li>Normalize all data to the endogenous reference gene gyrA. Use 2-&#916;&#916;CT method for data quantification15.</li>
	</ol>
	</li>
</ol>
6. Virulence assays
<ol>
	<li>Culture SE50336, 50336&#916;micC and 50336&#916;micC/pmicC in LB medium to early stationary phase (OD600 of 2-3) at 24 &#730;C, harvest by centrifugation, and dilute to appropriate CFU mL-1 in sterile PBS.</li>
	<li>For mice infections, dilute the cultured strains to 10 CFU/200 &#181;L, 102 CFU/200 &#181;L and 103 CFU/200 &#181;L gradient resuspensions. Infect groups of five 6-8 week old Balb/c mice per strain by subcutaneous injection. Inject the control group with 200 &#181;L of physiological saline.</li>
	<li>For chicken infections, dilute above three strains to 107 CFU/200 &#181;L, 108 CFU/200 &#181;L and 109 CFU/200 &#181;L gradient resuspensions. Infect groups of twenty 1-day-old chickens per strain by subcutaneous injection.</li>
	<li>Monitor signs of illness and deaths of experimental animals daily. Calculate the LD50 (median lethal dose) 14 d post-infection as described previously16. Process the data using data analysis software.</li>
	<li>In infection groups, collect the heart, liver, spleen, lung, and kidney of freshly dead chicks. Weigh 0.5 g of the above tissues separately and grind them with sterile operation. Dilute grinding samples gradually, spread them on LB plate and culture for 8-10 h at 37 &#730;C. Record the amount of Salmonella strains colonized in chick tissues.</li>
</ol>

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<li>Sharma, C. M., Darfeuille, F., Plantinga, T. H., Vogel, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((A+small+RNA+regulates+multiple+ABC+transporter+mRNAs+by+targeting+C%2FA-rich+elements+inside+and+upstream+of+ribosome-binding+sites%5BTitle%5D)+AND+%22Genes+and+Development%22%5BJournal%5D)">A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites.</a> Genes and Development. 21 (21), 2804-2817 (2007).</li>
<li>Boisset, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Staphylococcus+aureus+RNAIII+coordinately+represses+the+synthesis+of+virulence+factors+and+the+transcription+regulator+Rot+by+an+antisense+mechanism%5BTitle%5D)+AND+%22Genes+and+Development%22%5BJournal%5D)">Staphylococcus aureus RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator Rot by an antisense mechanism.</a> Genes and Development. 21 (11), 1353-1366 (2007).</li>
<li>Massé, E., Vanderpool, C. K., Gottesman, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Effect+of+RyhB+small+RNA+on+global+iron+use+in+Escherichia+coli%5BTitle%5D)+AND+%22Journal+of+Bacteriology%22%5BJournal%5D)">Effect of RyhB small RNA on global iron use in Escherichia coli.</a> Journal of Bacteriology. 187 (20), 6962-6971 (2005).</li>
<li>Papenfort, K., Vogel, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Regulatory+RNA+in+bacterial+pathogens%5BTitle%5D)+AND+%22Cell+Host+%26+Microbe%22%5BJournal%5D)">Regulatory RNA in bacterial pathogens.</a> Cell Host & Microbe. 8 (1), 116-127 (2010).</li>
</ol>

The authors have nothing to disclose.

S. Enteritidis is an important facultative intracellular pathogen that can infect young chickens and produces symptoms from enteritis to systemic infection and death17,18. In addition, S. Enteritidis causes latent infections in adult chickens and chronic carriers contaminate poultry products, resulting in food-borne infections in humans19. The pathogenic mechanism of S. Enteritidis remains to be further probed. T...

Non-coding small RNAs (sRNAs) are 40-400 nucleotides in length, which generally do not encode proteins but could be transcribed independently in bacterial chromosomes1,2,3. Most sRNAs are encoded in the intergenic regions (IGRs) between gene-coding regions and interact with target mRNAs through base-pairing actions, and regulate target genes expression at the post-transcriptional level4,5. They play important regulation roles in substance metabolism, outer membrane protein synthesis, quorum sensing and virulence gene expression5.
MicC is a 109-nucleotide small RNA transcript present in Escherichia coli and Salmonella enterica serovar Typhimurium, which could regulate multiple outer membrane protein expression such as OmpC, OmpD, OmpN, Omp35 and Omp366,7,8,9. MicC regulates the expression of OmpC by inhibiting ribosome binding to the ompC mRNA leader in vitro and it requires the Hfq RNA chaperone for its function in Escherichia coli6. In Salmonella Typhimurium, MicC silences ompD mRNA via a &#8804;12-bp RNA duplex within the coding sequence (codons 23-26) and then destabilizes endonucleolytic mRNA7. This regulation process is assisted by chaperone protein Hfq10. The OmpC is an abundant outer membrane protein that was thought to be important in environments where nutrient and toxin concentrations were&#160;high, such as in the intestine6. The OmpD porin is the most abundant outer membrane protein in Salmonella Typhimurium and represents about 1% of total cell protein11. OmpD is involved in adherence to human macrophages and intestinal epithelial cells12. MicC also represses the expression of both OmpC and OmpD porins. It is thought that MicC may regulate virulence. To explore new target genes regulated by MicC and study the virulence regulation function of micC, we cloned the micC gene in the Salmonella Enteritidis (SE) strain 50336, and then constructed the mutant 50336&#916;micC and the complemented mutant 50336&#916;micC/pmicC. Novel target genes were screened by qRT-PCR. The virulence of 50336&#916;micC was detected by mice and chicken infections.

<table><tbody><tr><td>dextrose</td><td>Sangon Biotech</td><td>A610219</td><td>for broth preparation</td></tr><tr><td>DNA purification kit</td><td>TIANGEN</td><td>DP214</td><td>for DNA purification</td></tr><tr><td>Ex Taq</td><td>TaKaRa</td><td>RR01A</td><td>PCR</td></tr><tr><td>KH&lt;sub&gt;2&lt;/sub&gt;PO&lt;sub&gt;4&lt;/sub&gt;</td><td>Sinopharm Chemical Reagent</td><td>10017608</td><td>for broth preparation</td></tr><tr><td>K&lt;sub&gt;2&lt;/sub&gt;HPO&lt;sub&gt;4&lt;/sub&gt;</td><td>Sinopharm Chemical Reagent</td><td>20032116</td><td>for broth preparation</td></tr><tr><td>L-Arabinose</td><td>Sangon Biotech</td><td>A610071</td><td>&amp;lambda;-Red recombination</td></tr><tr><td>Mini Plasmid Kit</td><td>TIANGEN</td><td>DP106</td><td>plasmid extraction</td></tr><tr><td>NaCl</td><td>Sinopharm Chemical Reagent</td><td>10019308</td><td>for broth preparation</td></tr><tr><td>(NH&lt;sub&gt;4&lt;/sub&gt;)&lt;sub&gt;2&lt;/sub&gt;SO&lt;sub&gt;4&lt;/sub&gt;</td><td>Sinopharm Chemical Reagent</td><td>10002917</td><td>for broth preparation</td></tr><tr><td>PrimeScript&lt;sup&gt;R&lt;/sup&gt;RT reagent Kit with gDNA Eraser&amp;nbsp;</td><td>TaKaRa</td><td>RR047</td><td>qRT-PCR</td></tr><tr><td>SYBR&lt;sup&gt;R&lt;/sup&gt; Premix Ex Taq II</td><td>TaKaRa</td><td>RR820</td><td>qRT-PCR</td></tr><tr><td>T4 DNA Ligase</td><td>NEB</td><td>M0202</td><td>Ligation</td></tr><tr><td>TRIzol&amp;nbsp;</td><td>Invitrogen</td><td>15596018</td><td>RNA isolation</td></tr><tr><td>Tryptone</td><td>Oxoid</td><td>LP0042</td><td>for broth preparation</td></tr><tr><td>Yeast extract</td><td>Oxoid</td><td>LP0021</td><td>for broth preparation</td></tr><tr><td>centrifuge</td><td>Eppendorf</td><td>5418</td><td>centrifugation</td></tr><tr><td>Electrophoresis apparatus</td><td>Bio-Rad</td><td>164-5050</td><td>Electrophoresis</td></tr><tr><td>&amp;nbsp;Electroporation System</td><td>Bio-Rad</td><td>165-2100</td><td>for bacterial transformation</td></tr><tr><td>Spectrophotometer</td><td>BioTek</td><td>Epoch</td><td>Absorbance detection</td></tr><tr><td>Real-Time PCR system</td><td>Applied Biosystems</td><td>7500 system</td><td>qRT-PCR</td></tr></tbody></table>

a non-coding small rna micc contributes to virulence in outer membrane proteins in salmonella enteritidis

A Non-Coding Small RNA MicC Contributes to Virulence in Outer Membrane Proteins in Salmonella Enteritidis

A non-coding small RNA (sRNA) is a new factor to regulate gene expression at the post-transcriptional level. A kind of sRNA MicC, known in Escherichia coli and Salmonella Typhimurium, could repress the expression of outer membrane proteins. To further investigate the regulation function of micC in Salmonella Enteritidis, we cloned the micC gene in the Salmonella Enteritidis strain 50336, and then constructed the mutant 50336&#916;micC by the &#955; Red-based recombination system and the complemented mutant 50336&#916;micC/pmicC carrying recombinant plasmid pBR322 expressing micC. qRT-PCR results demonstrated that transcription of ompD in 50336&#916;micC was 1.3-fold higher than that in the wild type strain, while the transcription of ompA and ompC in 50336&#916;micC were 2.2-fold and 3-fold higher than those in the wild type strain. These indicated that micC represses the expression of ompA and ompC. In the following study, the pathogenicity of 50336&#916;micC was detected by both infecting 6-week-old Balb/c mice and 1-day-old chickens. The result showed that the LD50 of the wild type strain 50336, the mutants 50336&#916;micC and 50336&#916;micC/pmicC for 6-week-old Balb/c mice were 12.59 CFU, 5.01 CFU, and 19.95 CFU, respectively. The LD50 of the strains for 1-day-old chickens were 1.13 x 109 CFU, 1.55 x 108 CFU, and 2.54 x 108 CFU, respectively. It indicated that deletion of micC enhanced virulence of S. Enteritidis in mice and chickens by regulating expression of outer membrane proteins.

Construction of the mutant 50336ΔmicC and complemented strain 50336ΔmicC /pmicC 
The micC gene clone result indicated that this gene was composed of 109 bp showing 100% identity with that of S. Typhimurium. Based on the sequence data, the deletion mutant 50336ΔmicC and the complemented mutant 50336ΔmicC/pmicC were constructed succes...

An &#955;-Red-mediated recombination system was used to create a deletion mutant of a small non-coding RNA micC.

A non-coding small RNA (sRNA) is a new factor to regulate gene expression at the post-transcriptional level. A kind of sRNA MicC, known in Escherichia ...

a-non-coding-small-rna-micc-contributes-to-virulence-outer-membrane

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