1. Diversity generating reverse transcriptase Reverse transcriptase an enzyme

2. Phage tail fiber Unknown protein Reverse transcriptase BPP Substitutions in action Directed by initiation of mutagenic homing

3. Alignment of BPP's VR vs TR

4. 1 in every million replications

5. BIP BMP

6. Not great identity but similar function Phage Tail fiber Unidentified protein Reverse Transcriptase TR VR Same Downstream order as in bordetella phages

7. TR VS VR in VHML What does it do??????????????

8. Vibrio phage with similar reverse transcriptase Vibrio phage with similar sequence but no reverse transcriptase

9. Understanding Phylogeny and Predicting New Class III Inteins Mobile Elements

10. Inteins – What are they? IntronsInteins

11. Tori et al (2010). J Biol Chem 285:2515-2526 HX amino acid HO-… Serine HO-CH 3 -… Threonine HS-CH 3 -… Cysteine Classes of Inteins (per splicing mechanism) Begins with Ser, Thr, or Cys

12. Class IClass II Tori et al (2010). J Biol Chem 285:2515-2526 Classes of Inteins (per splicing mechanism) Begins with Ser, Thr, or Cys Doesn't begin with Ser, Thr, or Cys HX amino acid HO-… Serine HO-CH 3 -… Threonine HS-CH 3 -… Cysteine

13. Class IClass IIClass III Tori et al (2010). J Biol Chem 285:2515-2526 Classes of Inteins (per splicing mechanism) Begins with Ser, Thr, or Cys Doesn't begin with Ser, Thr, or Cys Uses embedded Ser, Thr, or Cys HX amino acid HO-… Serine HO-CH 3 -… Threonine HS-CH 3 -… Cysteine

14. Tori et al (2010). J Biol Chem 285:2515-2526 How to recognize classes by sequence characteristics? Class IClass IIClass III Classes of Inteins (per splicing mechanism) Begins with Ser, Thr, or Cys Doesn't begin with Ser, Thr, or Cys Uses embedded Ser, Thr, or Cys

15. Recognition by conserved amino acid residues.

16. Recognition by conserved motifs.

17. Certain inteins are more similar than others.

18. What about extien similarity? Known inteins ????????? DnaB Intein Jumped in here?

19. Acknowledgements. This work would not have been possible without the support of: Jeff Elhai Raiha Tahir Mobile Elements Group

20. Farah Dahman Bioinformatics 301 MOBILE ELEMENTS EXISTENCE IN MYCOBACTERIOPHAGES

21. 5′-TTATC[a/t]GGGGT- 3’ MPEME1 MPEME2 HOW TO KNOW IF MOBILE ELEMENT FOUND “Mycobacteriophages BPs, Angel and Halo: comparative genomics reveals a novel class of ultra-small mobile genetic elements.”

22. Phages studied: Cluster F (average length- 57,422bp)  Fruit Loop, DotProduct, Ramsey, Yoshi, Boomer METHOD  

23. Run mobile element sequence through biobike into each bacteriophage TTATC[a/t]GGGGT Find closest match METHOD

24. Exact matches found in FruitLoop, Boomer, Yoshi Each has some form of end part of sequence, but not the TTAT piece Relatively close proximity of match within sequence compared to others Phages of Cluster F do share the same ultra small mobile elements

25. SAME 438 NUCLEOTIDES BUT DIFFERENT COORDINATES