Difference between revisions of "Part:BBa K4286322"

 
 
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<partinfo>BBa_K4286322 short</partinfo>
  
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In order to contain the infection of R.solani, we have identified RPMK1-2, which is critical to the infectivity of Rhizoctonia solani, as the taget of our first batch of RNAi targets.
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===Usage and Biology===
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RPMK1-2, which is one of the two PATHOGENICITY MAP KINASE 1 (PMK1) homologues, RPMK1-1 and RPMK1-2, is encoded by Rhizoctonia solani isolate R5 mitogen activated protein kinase gene. RPMK1 genes were strongly induced during the initial infection process. PMK1 homologues in other fungal pathogens are essential for the formation of appressorium, the fungal infection structures required for penetration of the plant cuticle, as well as invasive growth once inside the plant tissues and overall viability of the pathogen within the plant. Thus, we interfered with the expression of RPMK1-2 though this shRNA in order to prevent R.solani infection, suppress the viability of R.solani in rice, and ultimately cure rice sheath blight.
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===Design===
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Next, the RPMK1-2 sequences found by this method were analyzed, queried or predicted on the National Center for Biotechnology Information (NCBI) website whether there were multiple spliced versions of mRNA, and if there were, the homologous region was taken as the target region of RNAi interference target. However, it may be due to the lack of relevant research and literature support, and the corresponding mRNA has no variant. Also, the total nucleic acid database blast was carried out on the target CDS to query the similarity of homologous genes in adjacent species, and shRNA was designed in non-conserved regions to improve the species specificity of our shRNA and ensure biological safety.
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And then these gene fragments were analyzed by <html><a href="https://rnaidesigner.thermofisher.com/rnaiexpress/sort.do ">siRNA Design websites</a></html>. The program scans the DNA sequence of a gene fragment and calculates the binding energy of sense and antisense siRNAs based on the sequence pattern. The higher the score, the stronger the binding ability of the siRNA to the target sequence. Based on the principle of shRNA design, we selected the fragments with high potential siRNA activity from a series of sequences.
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For biosafety, the candidate RNAi fragments were submitted to the total mRNA database for blast, and the sequence similarity was compared. Focus on species with more than 90% similarity and their nucleic acid fragments to ensure that there is no matching of common species (human, rice, dog, wheat, etc.) to ensure the specificity of the sequence.
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Finally, the chosen RNAi fragment is assembled in the order of sense RNAi fragment—loop—antisense RNAi fragment.
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===Sequencing===
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===Usage and Biology===
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===Usage and Biology===
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<span class='h3bb'>Sequence and Features</span>
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<partinfo>BBa_K4286322 SequenceAndFeatures</partinfo>
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===Functional Parameters===
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<partinfo>BBa_K4286322 parameters</partinfo>
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===Assembly===
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We have confirmed that this siRNA sequence has a good binding ability to Rhizoctonia solani. The intrinsic order of this sequence is sense RNAi fragment — loop —  antisense RNAi fragment. This sequence was assembled in the pET28a (+) plasmid containing the IPTG-inducible phage T7 promoter and subsequently transferred into RNase-deficient E. coli HT115 (DE3). In our project, shRNA will be industrially produced by E. coli on a large scale, and shRNA will be purified and sprayed on rice fields to inhibit Rhizoctonia solani.
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==Characterization==
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===shRNA inhibits mycelium growth on leaves===
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To prove that our RNAi product can inhibit the infection of Rhizoctonia solani, we observed the growth of hyphae on leaves after spraying shRNA under a microscope (Figure 1.). At the same time, we also observed the leaves treated with shRNA after CNT binding (Figure 2.).
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<center>[[File:K4286107-Figure1.png]]</center>
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<center><b>Figure 1. Effect of spraying different shRNA on mycelial elongation without binding CNT</b></center>
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<center>[[File:K4286107-Figure2.png]]</center>
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<center><b>Figure 2. Effect of spraying different shRNA after binding CNT on mycelial elongation</b></center>
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After measuring the mycelium extension length in leaves under different treatments, the following statistical results are obtained (Figure 2.).
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<center>[[File:K4286107-Figure3.png]]</center>
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<center><b>Figure 3. Extension length of mycelium under different treatments.</b></center>
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<center>(a) The effect of spraying shRNA targeting key genes in infection process on mycelial extension without binding CNT. (b) Effect of spraying shRNA targeting key survival genes of Rhizoctonia solani on mycelial extension without CNT binding. (c) Effect of spraying shRNA targeting key genes in infection process after binding CNT on mycelial extension. (d) Effect of spraying shRNA targeting the key survival genes of Rhizoctonia solani after binding CNT on mycelial extension.</center>
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For spraying shRNA without CNT binding, the growth of mycelia on leaves was inhibited to some extent, but the inhibition effect was not ideal. For shRNA that inhibits the key genes in the infection process of R.solani, only the PG gene is inhibited; However, shRNA of key genes inhibiting the growth of Rhizoctonia solani had no significant effect.
 +
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After the shRNA was bound with CNT, it was sprayed. Compared with the control group's 21.5 mm mycelium length, the shRNA targeting the key genes in the infection process of Rhizoctonia solani could inhibit the extension of the mycelium to about 12.1 mm. For shRNA targeting the key genes of R.solani growth, the highest inhibition rate of hyphal extension was 40%.
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===Inhibition effect detected by qRT-PCR===
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For shRNA, we also verified its inhibition by the same method as for siRNA . At the same time, after binding CNTs, we also tested their effects (Figure 4.c, d).
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<center>[[File:K4286107-Figure4.png]]</center>
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<center><b>Figure 4. Inhibition effect of shRNA on target gene.</b></center>
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<center>(a) Silencing of target genes by spraying shRNA targeting key genes during infection without binding CNT. (b) Silencing of target genes by spraying shRNA targeting key survival genes of Rhizoctonia solani without CNT binding. (c) Silencing of target genes by spraying shRNA targeting key genes in the infection process after binding CNT. (d) Silencing effect of spraying shRNA targeting key survival genes of Rhizoctonia solani after binding CNT on target genes.</center>
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The results showed that when CNT was not bound, the average silencing efficiency of shRNAs targeting key genes in the infection process was about 0.33 compared with the control group, while the average silencing efficiency of shRNAs targeting key genes in the survival of Rhizoctonia solani was about 0.37; However, after the same amount of shRNA was bundled with CNT and sprayed, the expression of target genes was significantly inhibited compared with the control group and the group without CNT, and the average inhibition efficiency of the two types of shRNA was 0.59 and 0.66, respectively. To sum up, our shRNA inhibition effect is good, and binding CNT promotes the inhibition of shRNA against R.solani.
 +
 +
===Sustained inhibition===
 +
The essence of RNAi treatment is that sRNA molecules specifically recognize target genes in R.solani and then conduct post transcriptional silencing. Therefore, in order to verify the therapeutic effect of RNAi, we must measure the changes in the expression level of target genes in R.solani after spraying sRNA. We sprayed siRNA, shRNA and CNT shRNA respectively, and tested the effect of RNAi products through qRT-PCR for 5 consecutive days.
 +
 +
<center>[[File:K4286107-Figure5.jpeg]]</center>
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<center><b>Figure 5. Changes in the expression level of target genes. Blue represents the control group, red represents siRNA treatment, green represents shRNA treatment, and purple represents CNT shRNA treatment.</b></center>
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 +
For siRNA and shRNA treatment, the relative expression of target genes in Rhizoctonia solani decreased to the lowest at the third day, 0.144 and 0.103, respectively. But after that, the expression of target genes in both groups increased rapidly. Under the treatment of CNT shRNA, the expression of target gene decreased to 0.019 on the fourth day, and the effect lasted longer.
 +
To sum up, CNT shRNA has more obvious advantages in comparison with the size of the colony of Rhizoctonia solani growing on PDA medium, the growth degree of the mycelia on the leaves, the size of the diseased spot, the expression inhibition level of the target gene and the duration of the inhibition effect. Therefore, we look forward to its outstanding performance as our RNAi product.
 +
 +
===References===
 +
[1]Rao, T.B., Chopperla, R., Methre, R. et al. Pectin induced transcriptome of a Rhizoctonia solani strain causing sheath blight disease in rice reveals insights on key genes and RNAi machinery for development of pathogen derived resistance. Plant Mol Biol 100, 59–71 (2019). https://doi.org/10.1007/s11103-019-00843-9
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[2]Chen, X., Lili, L., Zhang, Y. et al. Functional analysis of polygalacturonase gene RsPG2 from Rhizoctonia solani, the pathogen of rice sheath blight. Eur J Plant Pathol 149, 491–502 (2017). https://doi.org/10.1007/s10658-017-1198-5

Latest revision as of 14:33, 12 October 2022

shRNA (RPMK1-2)-2

In order to contain the infection of R.solani, we have identified RPMK1-2, which is critical to the infectivity of Rhizoctonia solani, as the taget of our first batch of RNAi targets.

Usage and Biology

RPMK1-2, which is one of the two PATHOGENICITY MAP KINASE 1 (PMK1) homologues, RPMK1-1 and RPMK1-2, is encoded by Rhizoctonia solani isolate R5 mitogen activated protein kinase gene. RPMK1 genes were strongly induced during the initial infection process. PMK1 homologues in other fungal pathogens are essential for the formation of appressorium, the fungal infection structures required for penetration of the plant cuticle, as well as invasive growth once inside the plant tissues and overall viability of the pathogen within the plant. Thus, we interfered with the expression of RPMK1-2 though this shRNA in order to prevent R.solani infection, suppress the viability of R.solani in rice, and ultimately cure rice sheath blight.

Design

Next, the RPMK1-2 sequences found by this method were analyzed, queried or predicted on the National Center for Biotechnology Information (NCBI) website whether there were multiple spliced versions of mRNA, and if there were, the homologous region was taken as the target region of RNAi interference target. However, it may be due to the lack of relevant research and literature support, and the corresponding mRNA has no variant. Also, the total nucleic acid database blast was carried out on the target CDS to query the similarity of homologous genes in adjacent species, and shRNA was designed in non-conserved regions to improve the species specificity of our shRNA and ensure biological safety.

And then these gene fragments were analyzed by siRNA Design websites. The program scans the DNA sequence of a gene fragment and calculates the binding energy of sense and antisense siRNAs based on the sequence pattern. The higher the score, the stronger the binding ability of the siRNA to the target sequence. Based on the principle of shRNA design, we selected the fragments with high potential siRNA activity from a series of sequences.

For biosafety, the candidate RNAi fragments were submitted to the total mRNA database for blast, and the sequence similarity was compared. Focus on species with more than 90% similarity and their nucleic acid fragments to ensure that there is no matching of common species (human, rice, dog, wheat, etc.) to ensure the specificity of the sequence.

Finally, the chosen RNAi fragment is assembled in the order of sense RNAi fragment—loop—antisense RNAi fragment.

Sequencing

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Assembly

We have confirmed that this siRNA sequence has a good binding ability to Rhizoctonia solani. The intrinsic order of this sequence is sense RNAi fragment — loop — antisense RNAi fragment. This sequence was assembled in the pET28a (+) plasmid containing the IPTG-inducible phage T7 promoter and subsequently transferred into RNase-deficient E. coli HT115 (DE3). In our project, shRNA will be industrially produced by E. coli on a large scale, and shRNA will be purified and sprayed on rice fields to inhibit Rhizoctonia solani.

Characterization

shRNA inhibits mycelium growth on leaves

To prove that our RNAi product can inhibit the infection of Rhizoctonia solani, we observed the growth of hyphae on leaves after spraying shRNA under a microscope (Figure 1.). At the same time, we also observed the leaves treated with shRNA after CNT binding (Figure 2.).

K4286107-Figure1.png
Figure 1. Effect of spraying different shRNA on mycelial elongation without binding CNT
K4286107-Figure2.png
Figure 2. Effect of spraying different shRNA after binding CNT on mycelial elongation

After measuring the mycelium extension length in leaves under different treatments, the following statistical results are obtained (Figure 2.).

K4286107-Figure3.png
Figure 3. Extension length of mycelium under different treatments.
(a) The effect of spraying shRNA targeting key genes in infection process on mycelial extension without binding CNT. (b) Effect of spraying shRNA targeting key survival genes of Rhizoctonia solani on mycelial extension without CNT binding. (c) Effect of spraying shRNA targeting key genes in infection process after binding CNT on mycelial extension. (d) Effect of spraying shRNA targeting the key survival genes of Rhizoctonia solani after binding CNT on mycelial extension.

For spraying shRNA without CNT binding, the growth of mycelia on leaves was inhibited to some extent, but the inhibition effect was not ideal. For shRNA that inhibits the key genes in the infection process of R.solani, only the PG gene is inhibited; However, shRNA of key genes inhibiting the growth of Rhizoctonia solani had no significant effect.

After the shRNA was bound with CNT, it was sprayed. Compared with the control group's 21.5 mm mycelium length, the shRNA targeting the key genes in the infection process of Rhizoctonia solani could inhibit the extension of the mycelium to about 12.1 mm. For shRNA targeting the key genes of R.solani growth, the highest inhibition rate of hyphal extension was 40%.

Inhibition effect detected by qRT-PCR

For shRNA, we also verified its inhibition by the same method as for siRNA . At the same time, after binding CNTs, we also tested their effects (Figure 4.c, d).

K4286107-Figure4.png
Figure 4. Inhibition effect of shRNA on target gene.
(a) Silencing of target genes by spraying shRNA targeting key genes during infection without binding CNT. (b) Silencing of target genes by spraying shRNA targeting key survival genes of Rhizoctonia solani without CNT binding. (c) Silencing of target genes by spraying shRNA targeting key genes in the infection process after binding CNT. (d) Silencing effect of spraying shRNA targeting key survival genes of Rhizoctonia solani after binding CNT on target genes.

The results showed that when CNT was not bound, the average silencing efficiency of shRNAs targeting key genes in the infection process was about 0.33 compared with the control group, while the average silencing efficiency of shRNAs targeting key genes in the survival of Rhizoctonia solani was about 0.37; However, after the same amount of shRNA was bundled with CNT and sprayed, the expression of target genes was significantly inhibited compared with the control group and the group without CNT, and the average inhibition efficiency of the two types of shRNA was 0.59 and 0.66, respectively. To sum up, our shRNA inhibition effect is good, and binding CNT promotes the inhibition of shRNA against R.solani.

Sustained inhibition

The essence of RNAi treatment is that sRNA molecules specifically recognize target genes in R.solani and then conduct post transcriptional silencing. Therefore, in order to verify the therapeutic effect of RNAi, we must measure the changes in the expression level of target genes in R.solani after spraying sRNA. We sprayed siRNA, shRNA and CNT shRNA respectively, and tested the effect of RNAi products through qRT-PCR for 5 consecutive days.

K4286107-Figure5.jpeg
Figure 5. Changes in the expression level of target genes. Blue represents the control group, red represents siRNA treatment, green represents shRNA treatment, and purple represents CNT shRNA treatment.

For siRNA and shRNA treatment, the relative expression of target genes in Rhizoctonia solani decreased to the lowest at the third day, 0.144 and 0.103, respectively. But after that, the expression of target genes in both groups increased rapidly. Under the treatment of CNT shRNA, the expression of target gene decreased to 0.019 on the fourth day, and the effect lasted longer. To sum up, CNT shRNA has more obvious advantages in comparison with the size of the colony of Rhizoctonia solani growing on PDA medium, the growth degree of the mycelia on the leaves, the size of the diseased spot, the expression inhibition level of the target gene and the duration of the inhibition effect. Therefore, we look forward to its outstanding performance as our RNAi product.

References

[1]Rao, T.B., Chopperla, R., Methre, R. et al. Pectin induced transcriptome of a Rhizoctonia solani strain causing sheath blight disease in rice reveals insights on key genes and RNAi machinery for development of pathogen derived resistance. Plant Mol Biol 100, 59–71 (2019). https://doi.org/10.1007/s11103-019-00843-9

[2]Chen, X., Lili, L., Zhang, Y. et al. Functional analysis of polygalacturonase gene RsPG2 from Rhizoctonia solani, the pathogen of rice sheath blight. Eur J Plant Pathol 149, 491–502 (2017). https://doi.org/10.1007/s10658-017-1198-5