[Comparative analysis of clustered regularly interspaced short palindromic repeats (CRISPRs) loci in the genomes of halophilic archaea].
OBJECTIVE
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is a widespread system that provides acquired resistance against phages in bacteria and archaea. Here we aim to genome-widely analyze the CRISPR in extreme halophilic archaea, of which the whole genome sequences are available at present time.


METHODS
We used bioinformatics methods including alignment, conservation analysis, GC content and RNA structure prediction to analyze the CRISPR structures of 7 haloarchaeal genomes.


RESULTS
We identified the CRISPR structures in 5 halophilic archaea and revealed a conserved palindromic motif in the flanking regions of these CRISPR structures. In addition, we found that the repeat sequences of large CRISPR structures in halophilic archaea were greatly conserved, and two types of predicted RNA secondary structures derived from the repeat sequences were likely determined by the fourth base of the repeat sequence.


CONCLUSIONS
Our results support the proposal that the leader sequence may function as recognition site by having palindromic structures in flanking regions, and the stem-loop secondary structure formed by repeat sequences may function in mediating the interaction between foreign genetic elements and CAS-encoded proteins.
Zhang
Fan
F
Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China. fanz07@yahoo.com.cn
Zhang
Bing
B
Xiang
Hua
H
Hu
Songnian
S
D001105:Archaea / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D001483:Base Sequence; D002712:Chlorides / Q000378:metabolism*; D019295:Computational Biology; D019641:DNA, Archaeal / Q000737:chemistry / Q000235:genetics; D020745:Genome, Archaeal; D055029:Inverted Repeat Sequences; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016415:Sequence Alignment
D002712:Chlorides; D019641:DNA, Archaeal; C001599:chlorite