Endogenous Gene Regulation as a Predicted Main Function of Type I-E CRISPR/Cas System in E. coli

Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry
Bojan BozicMarko Djordjevic

Abstract

CRISPR/Cas is an adaptive bacterial immune system, whose CRISPR array can actively change in response to viral infections. However, Type I-E CRISPR/Cas in E. coli (an established model system), appears not to exhibit such active adaptation, which suggests that it might have functions other than immune response. Through computational analysis, we address the involvement of the system in non-canonical functions. To assess targets of CRISPR spacers, we align them against both E. coli genome and an exhaustive (~230) set of E. coli viruses. We systematically investigate the obtained alignments, such as hit distribution with respect to genome annotation, propensity to target mRNA, the target functional enrichment, conservation of CRISPR spacers and putative targets in related bacterial genomes. We find that CRISPR spacers have a statistically highly significant tendency to target i) host compared to phage genomes, ii) one of the two DNA strands, iii) genomic dsDNA rather than mRNA, iv) transcriptionally active regions, and v) sequences (cis-regulatory elements) with slower turn-over rate compared to CRISPR spacers (trans-factors). The results suggest that the Type I-E CRISPR/Cas system has a major role in transcription regulation of ...Continue Reading

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Citations

Feb 23, 2020·Genes·Liu HeEdward L Bolt
Sep 26, 2019·Frontiers in Microbiology·Ognjen MilicevicMarko Djordjevic
Dec 5, 2020·Scientific Reports·Simran Krishnakant KushwahaSandhya Amol Marathe
Sep 7, 2021·International Microbiology : the Official Journal of the Spanish Society for Microbiology·Noemí M GuzmánFrancisco J M Mojica

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Methods Mentioned

BETA
restriction modification
phylogenetic footprinting
RNA-seq

Software Mentioned

PANTHER
SAS

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