Prediction of CRISPR-Cas Targets in Salmonella Typhimurium

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is an immunity system that was discovered in E. Coli. The CRISPR system consists of short repeats of palindromic DNA which is interspaced by non identical spacer sequences. In early 2000s, it was found that these spacer sequences were identical to viral DNA, especially bacteriophage DNA. A number of genes, called the Cas genes (CRISPR associated) were also identified. The Cas genes transcribe and translate to Cas proteins. These Cas genes are essentially helicases and nucleases which unwind and cut DNA respectively. Along with CRISPR sequences, they form CRISPR-Cas system. Spacer sequences direct the CRISPR-Cas complex towards a viral DNA, resulting into degradation of viral DNA by Cas proteins.

It has to be noted that CRISPR-Cas system provides acquired immunity to bacteria. This is because the spacer sequences are derived from previous viral infections, and any such viral infection leads to an addition of spacer sequence in the spacer array.

Until recently, it was observed that CRISPR-Cas system only affects external viral DNA. But it has been observed that CRISPR-Cas system can also regulate self genes, in addition to viral DNA.

The study of these endogenous gene targets of CRISPR-Cas system is essential, as these genes may be involved in various biological pathways such as biofilm formation, pathogenicity etc in prokaryotes, similar to how miRNA and small RNA regulate the transcription of various endogenous genes.

This thesis is an attempt to predict the self gene targets of CRISPR 1 and CRISPR 2 systems in Salmonella Typhimurium str. 14028s. Various methodologies from RNAi prediction tools have inspired this project