Part:BBa_K4147016

siRNA designed to target RXLR gene of P. capsici

This gene target the RXLR gene of P. capsici. The RXLR gene encodes for RXLR effectors, a protein produced by P. capsici which suppresses the plant's natural defense system.

Usage and biology

P. capsici is one of the most devastating plant pathogens [1]. This is mainly due to the fact that this organism contains effector proteins that are able to suppress the plant immune system [2]. Among these proteins, one of the most studied is the RXLR effectors [3].

The RXLR effectors of P. capsici are critical for its pathogenicity [3, 4]. In addition, studies have reported that silencing this gene reduces the pathogenicity of the oomycete [3].

Thermodynamic properties

In collaboration with the iGEM Tec-Monterrey 2022 team, we performed an evaluation of the siRNA sequence we designed. For this we sent the mRNA of the gene we plan to silence (RXLR of P. capsici). And with the help of the software they developed, we obtained a hybridization Gibbs Free Energy of approximately -32.9 kcal/mol, the lower this value the better. Since it indicates that the hybridization will be a spontaneous reaction.

Free Gibbs Energy analysis of possible siRNAs that target RXLR gene of P. capsici. Our designed siRNA showed a Gibbs Free Energy of -32.9 kcal/mol. Which indicates that the hybridization reaction will be a spontaneous reaction.

Likewise, the in silico analysis showed a relative efficiency of hybridization of 93%. The software developed by the Tec-Monterrey 2022 team evaluates all possible siRNAs and according to the analysis of the thermodynamic properties of each siRNA assigns a value between 0 and 100, where 100 is an almost perfect site to hybridize and 0 is a bad site to hybridize.

Analysis of possible siRNAs that target RXLR gene of P. capsici. Our designed siRNA showed a relative efficiency of hybridization of 93%.

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]

References

1. Barchenger DW, Lamour KH, Bosland PW. Challenges and strategies for breeding resistance in Capsicum annuum to the multifarious pathogen, Phytophthora capsici. Frontiers in plant science. 2018;9:628. 2. He Q, McLellan H, Boevink PC, Birch PRJ. All roads lead to susceptibility: The many modes of action of fungal and oomycete intracellular effectors. Plant Communications. 2020;1(4):100050. 3. Cheng W, Lin M, Chu M, κ.ά. RNAi-Based Gene Silencing of RXLR Effectors Protects Plants Against the Oomycete Pathogen Phytophthora capsici. Molecular Plant-Microbe Interactions. 2022;35(6):440–449. 4. Jiang RHY, Tyler BM. Mechanisms and evolution of virulence in oomycetes. Annual review of phytopathology. 2012;50:295–318.