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OJBTM
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, 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.
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