Diversity generating reverse transcriptase Reverse transcriptase an enzyme.

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 InteinsMobile Elements

Inteins – What are they?

Introns Inteins

Tori et al (2010). J Biol Chem 285:2515-2526

HX amino acid HO-… SerineHO-CH3-… ThreonineHS-CH3-… Cysteine

Classes of Inteins (per splicing mechanism)

Begins withSer, Thr, or Cys

Class I Class II

Tori et al (2010). J Biol Chem 285:2515-2526

Classes of Inteins (per splicing mechanism)

Begins withSer, Thr, or Cys

Doesn't begin withSer, Thr, or Cys

HX amino acid HO-… SerineHO-CH3-… ThreonineHS-CH3-… Cysteine

Class I Class II Class III

Tori et al (2010). J Biol Chem 285:2515-2526

Classes of Inteins (per splicing mechanism)

Begins withSer, Thr, or Cys

Doesn't begin withSer, Thr, or Cys

Uses embeddedSer, Thr, or Cys

HX amino acid HO-… SerineHO-CH3-… ThreonineHS-CH3-… Cysteine

Tori et al (2010). J Biol Chem 285:2515-2526

How to recognize classes by sequence characteristics?

Class I Class II Class III

Classes of Inteins (per splicing mechanism)

Begins withSer, Thr, or Cys

Doesn't begin withSer, Thr, or Cys

Uses embeddedSer, 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 DahmanBioinformatics 301

MOBILE ELEMENTS EXISTENCE IN

MYCOBACTERIOPHAGES

• 5′-TTATC[a/t]GGGGT-3’MPEME1MPEME2

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