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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
