Part:BBa_K4286909
shRNA molecules that can silence the gene encoding Ubiquitin ligase E3.
The second batch of shRNAs is designed for inhibiting the house keeping genes of R.solani. Thus, we have identified Ubiquitin ligase E3, and Importin β1, which is critical to the survival of Rhizoctonia solani, as the target of shRNA.
Usage and Biology
Ubiquitin-proteasome pathway is the most important protein degradation pathway in all known eukaryotes. Ubiquitin ligase E3 participates in a variety of physiological processes in cells by regulating ubiquitination, and has the ability to link target proteins to specific E2. Ubiquitin ligase E3 determines the specific recognition of target proteins and plays an important role in the ubiquitin pathway. Thus, we designed this shRNA molecule so as to disrupt protein degradation mechanisms as well as metabolism.
Design
Next, the Ubiquitin ligase E3 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
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE 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.).
After measuring the mycelium extension length in leaves under different treatments, the following statistical results are obtained (Figure 2.).
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).
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.
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]Zhou B, Bailey A, Niblett CL, Qu R. Control of brown patch (Rhizoctonia solani) in tall fescue (Festuca arundinacea Schreb.) by host induced gene silencing. Plant Cell Rep. 2016 Apr;35(4):791-802. doi: 10.1007/s00299-015-1921-7. Epub 2016 Jan 22. PMID: 26800976.
[2]Bilir Ö, Göl D, Hong Y, McDowell JM, Tör M. Small RNA-based plant protection against diseases. Front Plant Sci. 2022 Aug 18;13:951097. doi: 10.3389/fpls.2022.951097. PMID: 36061762; PMCID: PMC9434005.
[3]Rabuma T, Gupta OP, Chhokar V. Recent advances and potential applications of cross-kingdom movement of miRNAs in modulating plant's disease response. RNA Biol. 2022;19(1):519-532. doi: 10.1080/15476286.2022.2062172. Epub 2021 Dec 31. PMID: 35442163; PMCID: PMC9037536.
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