Transcript On the evolution of thymidine synthesis

On the evolution of
thymidine synthesis:
lateral gene transfer, viral
involvement and early life
Adi Stern
Under the supervision of Tal Pupko
What makes DNA what it is?


Deoxy-nucleotides
Thymidine
Thymidylate Synthase (Thy)
►Synthesizes
dTMP (T), one of the DNA building blocks
The canonical Thy enzyme


Almost all Eukarya, E.coli
The mystery of the slime mold (Mycetozoa)
ThyA
An alternative Thy enzyme

In 1989/2002, an alternative mechanism for Thymidylate
synthesis was discovered, and the enzyme was named
ThyX – flavin dependent
ThyA
ThyX
ThyX distribution
Lateral gene
transfer
(LGT)
-
Myllykallio et al. Science (297) 2002
Lateral Gene Transfer (LGT) is any
process in which an organism transfers
genetic material to another organism that
is not its offspring
Evolution of thymidylate
synthases
Goals
1.
2.
3.
Quantify and locate events of LGT
Find origins of each LGT event using
gene trees
When did Thy originate?
Studying Thy LGT
Map ThyA and ThyX on the species tree
 Reconstruct ThyA / ThyX / both at each
ancestor

Thy mapping
on species
tree:
BLAST against
~400 whole
genomes
Legend:
- ThyA
- ThyX
- ThyX & Thy A
Deinococcales: the
coloring means there
are some deinococci
which encode for ThyA
and others for ThyX
Thy mapping
on species tree
How to
reconstruct ?
Evolutionary
models
What are evolutionary models
useful for?
Which one is more likely?
X
X
A
A
A
A
A
A+ X
X
A
A
A
A
A
X
X
X
A
A
A
A
ThyX gain
ThyA loss
ThyX loss
ThyX gain,
ThyA loss
X
A
A
X
A
Evolutionary models

The aim of an evolutionary model: to describe
(often in probabilistic terms) the evolutionary
biological reality
A
C
G
T
A  0.73 0.08 0.11 0.08 


C  0.11 0.8 0.01 0.08 
G  0.08 0.2 0.68 0.04 



T  0.02 0.01 0.1 0.87 
Likelihood


An evolutionary model enables us to
compute the likelihood that a certain
scenario describes the biological reality we
observe.
Learn the different probabilities from the
data
A
A
A
X
A
A
A+ X
X
X
A
A
X
A
A
A
A
X
A
A
X
X
A
A
A X
A
A gain-loss evolutionary model
A
A
X
A+X
X
 1
0
0  2
3
3
A+X
1
2
 3   4
An evolutionary model
A
A
X
A+X
X
 1
0
0  2
3
3
Rate of loss
μ1, μ2, μ3, μ4 are maximum-likelihood estimates
A+X
1
2
 3   4
Rate of gain
Results


rate of loss >> rate of gain
rate of gain of ThyA > gain of ThyX
Results – Maximum Likelihood
Reconstruction
At least:
14 LGT events
where ThyA
was swapped
by ThyX (or
vice versa)
Origin of Mycetozoa ThyX
To find the
origin of an LGT,
we look at the
gene tree based
on the multiple
sequence
alignment of
one of the genes
Two possible explanations
1.
2.
Mycetozoa eat bacteria 
digested some bacterial DNA
The ancestor of mitochondria
is known to be an
α-proteobacteria  mitochondrial
involvement?
Viruses
Myoviridae
Viral sequences’
distribution
Siphoviridiae
Herpesviridae
Podoviridae
Early life
Beginning of life - RNA world

“…The universal ancestor is not a discrete
entity. It is, rather, a diverse community of
cells that survives and evolves as a
biological unit…“ (Woese, 1998)
LUCA – the last
universal common
ancestor, is a
communal
“swamp”
LGT
RNA  DNA world

Controversy around how DNA evolved
Bacteria
Eukarya
Archaea
Founder Viruses

“…Viruses played a critical role in the
emergence of DNA…several independent
transfers [from viruses] produced the two cell
types (prokaryote/eukaryote) and the three
cellular domains …” (Forterre PNAS(103) 2006)
Bacteria
virus
Eukarya
Archaea
Viruses and Thy in early life
ThyA gene tree
T4 like phages
hosts
T4 like
phages
ThyA gene tree
T4-like
phages
?
Archaea
Bacteria
(hosts)
Eukarya
A model for Thy evolution in
early life
RNA world and RNA viruses
LGT
Viruses modify their genome to
evade host defense
Thymidine
Thymidylate
synthase
dCMP hydroxymethylase )CH(

In fact – T4 like phages use a similar tactic
today!
Thymidine
Thymidine
Hydroxymethylated
cytosine
CH

Interestingly, CH and ThyA are homologs
(sequentially and structurally)
Song et al. EMBO J (18) 1999
Summary
Open questions:
 When did ThyX
come in and how?
 Who predated
who?
 Why is there so
much LGT between
these two
enzymes?
Thank you ….




Dr. Tal Pupko
Shaul Shaul, Itay Mayrose
Dr. Uri Gophna
Lab members:
Adi Doron
Eyal Privman
Nimrod Rubinstein
Osnat Penn
Dudu Burstein
Ofir Cohen