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Diversity generating
reverse transcriptase
Reverse transcriptase an enzyme
BPP Substitutions in action
Reverse
transcriptase
Phage tail fiber
Directed by
initiation of
mutagenic
homing
Unknown
protein
Alignment of BPP's VR vs TR
1 in every million
replications
BMP
BIP
Not great identity but similar function
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?
Introns
Inteins
Classes of Inteins
(per splicing mechanism)
Begins with
Ser, Thr, or Cys
HX
amino acid
HO-…
Serine
HO-CH3-… Threonine
HS-CH3-… Cysteine
Tori et al (2010). J Biol Chem 285:2515-2526
Classes of Inteins
(per splicing mechanism)
Class I
Class II
Begins with
Ser, Thr, or Cys
Doesn't begin with
Ser, Thr, or Cys
HX
amino acid
HO-…
Serine
HO-CH3-… Threonine
HS-CH3-… Cysteine
Tori et al (2010). J Biol Chem 285:2515-2526
Classes of Inteins
(per splicing mechanism)
Class I
Class II
Class III
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-CH3-… Threonine
HS-CH3-… Cysteine
Tori et al (2010). J Biol Chem 285:2515-2526
Classes of Inteins
(per splicing mechanism)
Class I
Class II
Class III
Begins with
Ser, Thr, or Cys
Doesn't begin with
Ser, Thr, or Cys
Uses embedded
Ser, Thr, or Cys
How to recognize classes by
sequence characteristics?
Tori et al (2010). J Biol Chem 285:2515-2526
Recognition by conserved
amino acid residues.
Recognition by conserved
motifs.
Certain inteins are more
similar than others.
What about extien similarity?
?????????
DnaB Intein
Jumped in
here?
Known
inteins
Acknowledgements.
This work would not have been possible without the
support of:
 Jeff Elhai
 Raiha Tahir
 Mobile Elements Group
MOBILE ELEMENTS
EXISTENCE IN
MYCOBACTERIOPHAGES
Farah Dahman
Bioinformatics 301
HOW TO KNOW IF MOBILE
ELEMENT FOUND
• 5′-TTATC[a/t]GGGGT-
3’
MPEME1
MPEME2
“Mycobacteriophages BPs,
Angel and Halo:
comparative genomics
reveals a novel class of
ultra-small mobile genetic
elements.”
METHOD
• 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
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