- Article -
| In Silico Biology 9, 0021 (2009); ©2009, Bioinformation Systems e.V. |
Assessment of the evolutionary origin and possibility of CRISPR-Cas (CASS) mediated RNA interference pathway in Vibrio cholerae O395
Sajib Chakraborty1, T. M. Zaved Waise1, Faizule Hassan1, Yearul Kabir2, Mark A. Smith3 and Mohammad Arif1*
1 Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
2 Department of Family Sciences, College for Women, Kuwait University, Kuwait
3 Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
* Corresponding author
Email: marif@univdhaka.edu
Edited by E. Wingender; received December 27, 2008; revised February 25, 2009; accepted May 21, 2009; published June 14, 2009
Abstract
Bacteria have developed several defense mechanisms against bacteriophages over evolutionary time, but the concept of prokaryotic RNA interference mediated defense mechanism against phages and other invading genetic elements has emerged only recently. Clustered regularly interspaced short palindromic repeats (CRISPR) together with closely associated genes (cas genes) constitute the CASS system that is believed to provide a RNAi-like defense mechanism against bacteriophages within the host bacterium. However, a CASS mediated RNAi-like pathway in enteric pathogens such as Vibrio cholerae O395 or Escherichia coli O157 have not been reported yet. This study specifically was designed to investigate the possibility and evolutionary origin of CASS mediated RNAi-like pathway in the genome of a set of enteric pathogens, especially V. cholerae. The results showed that V. cholerae O395 and also other related enteric pathogens have the essential CASS components (CRISPR and cas genes) to mediate a RNAi-like pathway. The functional domains of a V. cholerae Cas3 protein, which is believed to act as a prokaryotic Dicer, was revealed and compared with the domains of eukaryotic Dicer proteins. Extensive homology in several functional domains provides significant evidence that the Cas3 protein has the essential domains to play a vital role in RNAi like pathway in V. cholerae. The secondary structure of the pre-siRNA for V. cholerae O395 was determined and its thermodynamic stability also reinforced the previous findings and signifies the probability of a RNAi-like pathway in V. cholerae O395.
Keywords: CRISPR, cas genes, prokaryotic RNA interference, Vibrio cholerae O395