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OJBTM
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,
ABSTRACT
Chatterjee R, Dutta A, Chaudhuri K., Molecular evolution of archaeal
CRISPR and Cas genes, Online J Bioinformatics, 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.