Analysis Of CRISPR Structures In Pathogen Bacteria Strains Based On CRISPR Database

Clustered regularly interspaced short palindromic repeats(CRISPR),is a set of defense system to resist phage interference that most bacteria and archaea evolved under the survival pressure.Firstly,this research determines 549 pathogenic bacterial strain of 2612 bacteria in the CRISPR database according to VFDB,PHI-base and NMPDR pathogenic bacteria database,and then makes a comparative analysis to the number and source of the spacer sequences in CRISPR structure of pathogenic bacterial strain and total bacterial strain by BLAST comparison.Finally,the 109 CRISPR loci of 50 pathogenic strains were subjected to multiple sequence comparison of flanking sequences and RNA secondary structure prediction of repeat sequences by clustalw,MEGA5.0 software and RNA structure website.The results of the comparative analysis of the number and source of the spacer sequences in CRISPR structure of pathogenic bacterial strain and total bacterial strain were shown,in the pathogenic bacterial strain,bacterial strain's proportion containing CRISPR structure is 48.5%,and is slightly higher than the proportion of the total bacterial strain;but the number of spacer sequence has significant difference between total bacterial strain and pathogenic bacterial strain,and spacer sequence distribution situation of pathogenic bacterial strain is lower than the average level of bacteria;the spacer sequence of virus source in the pathogenic bacterial strain's CRISPR structure occupies a larger proportion than plasmid source.After comparing multiple flanking sequences across 109 loci of 50 pathogen strains and predicting secondary structure of RNA,it is discovered that 109 CRISPR loci can be divided into five groups.However,grouping of flanking sequences differs during their evolution in different CRISPR loci of the same pathogen strain.Meanwhile,a segment of leader sequences rich in AT has been found in the flanking sequence.Features of intra-genome repetitive sequences are compared according to grouping of flanking sequences,and flanking sequences are thereby found to be correlated to repetitive sequences in pathogen strains.The RNA secondary structures of repetitive sequences are mostly stem-loop structures in most pathogen strains,so spacer sequences generally interact with exogenous DNA or RNA through a single"repeat-spacer".Through the analysis of the bacterial strain's CRISPR structure,we can further understand pathogenic bacteria's life and acquired immune defense system,and can provide guidance and help for the pathogenicity study of animal,plant and human pathogen.