Search for CRISPRs in mycobacteriophages

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Presentation transcript:

Search for CRISPRs in mycobacteriophages Rachel Siefring

Phage life cycle

What is a CRISPR? Figure 1: Figure 1 of Westra et al (2012). Simple representation of

How CRISPRs work repeat Figure 1C from Sorek et al (2008). Repeat: 24 to 47 bp Spacers: 26 to 72bp Figure 1C from Sorek et al (2008).

Seed et al 2013 V. cholerae O1 antigen receptor V. cholerae phage ICP1

Seed et al 2013 V. cholerae phage ICP1 Mutated O1 antigen receptor

CRISPR in ICP1

Looking for CRISPRs in BioBIKE

Looking for CRISPRs in BioBIKE

Mycobacteriophage Giles First repeat in mycobacteriophage Giles Second repeat in mycobacteriophage Giles Third repeat in mycobacteriophage Giles First repeat: 240 nuc difference. The 40nuc after the second repeat is more likely… Second repeat: There’s a 120 nucleotide difference from the beginning of the first repeat to the beginning of the second repeat. Third repeat: There’s over 700 nuc difference between these two repeats. Not likely

Mycobacteriophage RedRock 62nt repeat. My algorithm divided it into 3 different 23nt repeats.

Other results Searched for CRISPRs in 17 Cluster A mycobacteriophages No 23nuc repeats

Future improvements Improve my algorithm so that it only catches spacers of a specific length (35 to 40 nuc). Use this algorithm to search for CRISPRs in all phage on BioBIKE.

References Sorek, R., et al. (2008). CRISPR – a widespread system that provides acquired resistance against phages in bacteria and archaea. Nature Reviews Microbiology. 6: 181-186. Seed, K., et al. (2013). A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity. Nature. 494: 489-491. http://www.nature.com.proxy.library.vcu.edu/nature/journal/v494/n7438/ full/nature11927.html#supplementary-information Samson, J. E., et al. (2013). Revenge of the phages: defeating bacterial defenses. Nature Reviews Microbiology. 11: 675-687. http://www.nature.com.proxy.library.vcu.edu/nrmicro/journal/v11/n10/ful l/nrmicro3096.html Westra, et al. (2012). The CRISPRs, They are a-changin': How Prokaryotes Generate Adaptive Immunity. Annu. Rev. Genet. 46: 311-319.