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Diversity generating reverse transcriptase

Reverse transcriptase an enzyme. Diversity generating reverse transcriptase. BPP Substitutions in action. Reverse transcriptase. Phage tail fiber. Unknown protein. Directed by initiation of mutagenic homing. Alignment of BPP's VR vs TR. 1 in every million replications. BMP. BIP.

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Diversity generating reverse transcriptase

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  1. Reverse transcriptase an enzyme Diversity generating reverse transcriptase

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

  3. Alignment of BPP's VR vs TR

  4. 1 in every million replications

  5. BMP BIP

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

  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? Introns Inteins

  11. Classes of Inteins(per splicing mechanism) Begins withSer, Thr, or Cys HX amino acid HO-… SerineHO-CH3-…ThreonineHS-CH3-… Cysteine Tori et al (2010). J Biol Chem 285:2515-2526

  12. Classes of Inteins(per splicing mechanism) Class I Class II Begins withSer, Thr, or Cys Doesn't begin withSer, Thr, or Cys HX amino acid HO-… SerineHO-CH3-…ThreonineHS-CH3-… Cysteine Tori et al (2010). J Biol Chem 285:2515-2526

  13. Classes of Inteins(per splicing mechanism) Class I Class II Class III Begins withSer, Thr, or Cys Doesn't begin withSer, Thr, or Cys Uses embeddedSer, Thr, orCys HX amino acid HO-… SerineHO-CH3-…ThreonineHS-CH3-… Cysteine Tori et al (2010). J Biol Chem 285:2515-2526

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

  15. Recognition by conserved amino acid residues. Histidine Asparagine Histidine Glycine Glycine G G H H N C T W Cysteine Threonine Tryptophan

  16. Recognition by conserved motifs.

  17. Certain inteins are more similar than others.

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

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

  20. Mobile elements existence in mycobacteriophages Farah DahmanBioinformatics 301

  21. How to know if mobile element found • 5′-TTATC[a/t]GGGGT-3’MPEME1MPEME2 “Mycobacteriophages BPs, Angel and Halo: comparative genomics reveals a novel class of ultra-small mobile genetic elements.”

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

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

  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

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