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Online Journal of Bioinformatics


Volume 8 (2):189-204, 2007

Molecular evolution of archaeal CRISPR and Cas genes


Chatterjee R, Dutta A, Chaudhuri K



Molecular & Human Genetics Division Indian Institute of Chemical Biology, Jadavpur, Kolkata-700 032, India.




Chatterjee R, Dutta A, Chaudhuri K., Molecular evolution of archaeal CRISPR and Cas genes, Onl J Bioinform, 8 (2):189-204, 2007. Clustered regularly interspaced short palindrome repeats (CRISPR), recognized in many prokaryotes, especially in archaea are always associated with Cas (CRISPR-associated) proteins. CRISPR in 38 completely sequenced archaeal genomes were investigated. Homologs of reported Cas genes were searched for in these genomes. Evolution of CRISPR-Cas system was studied using GC-content, codon usage, relative synonymous codon usage (RSCU), amino acids usage (AAU), multivariate analysis and molecular phylogenetic analysis (MPA). GC contents of CRISPR and those of the corresponding genome are highly correlated. GC content, codon usage, RSCU and AAU of Cas genes are significantly similar to those of the rest of the genome. Multivariate analysis on RSCU and AAU suggests sources of variation along Axis1 for GC3 and hydrophobicity respectively in most archaea, which are also reflected for Cas genes of the corresponding genome. These observations show a similarity in nucleotide composition of CRISPR-Cas system with their corresponding genome. MPA based on the divergence of the distance showed that matrices for 16SrRNA-Cas1 and 16SrRNA-RNA polymerase were significantly different, and MPA based on tree distance showed that Robinson-Foulds symmetric difference and the Branch score distances of 16SrRNA-Cas1 were clearly different from those for 16SrRNA-RNA polymerase, suggesting horizontal gene transfer (HGT) event. This data led us to conclude that Cas genes suffered HGT event long back in archaea and its adaptation towards host genome has occurred during the course of evolution.


Keywords: CRISPR, Cas genes, GC content, codon usage, amino acids usage, archaea and molecular phylogeny.