Diversity generating reverse transcriptase Reverse transcriptase an enzyme

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

Alignment of BPP's VR vs TR

1 in every million replications

BIP BMP

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

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

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

Understanding Phylogeny and Predicting New Class III Inteins Mobile Elements

Inteins – What are they? IntronsInteins

Tori et al (2010). J Biol Chem 285: 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

Class IClass II Tori et al (2010). J Biol Chem 285: 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

Class IClass IIClass III Tori et al (2010). J Biol Chem 285: 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

Tori et al (2010). J Biol Chem 285: 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

Recognition by conserved amino acid residues.

Recognition by conserved motifs.

Certain inteins are more similar than others.

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

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

Farah Dahman Bioinformatics 301 MOBILE ELEMENTS EXISTENCE IN MYCOBACTERIOPHAGES

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.”

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

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

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

SAME 438 NUCLEOTIDES BUT DIFFERENT COORDINATES