on the evolution of thymidine synthesis: lateral gene transfer, viral involvement and early life
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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. - PowerPoint PPT PresentationTRANSCRIPT
On the evolution of On the evolution of thymidine synthesis: thymidine synthesis:
lateral gene transfer, viral lateral gene transfer, viral involvement and early lifeinvolvement and early life
Adi SternUnder the supervision of Tal Pupko
What makes DNA what it What makes DNA what it is?is?
Deoxy-nucleotidesDeoxy-nucleotides ThymidineThymidine
Thymidylate Synthase Thymidylate Synthase (Thy)(Thy)
►Synthesizes dTMP (T), one of the DNA building blocksSynthesizes dTMP (T), one of the DNA building blocks
The canonical Thy The canonical Thy enzymeenzyme
ThyA
Almost all Eukarya, E.coliAlmost all Eukarya, E.coli The mystery of the slime mold The mystery of the slime mold (Mycetozoa)(Mycetozoa)
An alternative Thy An alternative Thy enzymeenzyme
In 1989/2002, an alternative mechanism for Thymidylate In 1989/2002, an alternative mechanism for Thymidylate synthesis was discovered, and the enzyme was named synthesis was discovered, and the enzyme was named ThyX ThyX – flavin dependent– flavin dependent
ThyA
ThyX
-
ThyX distributionThyX distribution
Myllykallio et al. Science (297) 2002
Lateral gene
transfer (LGT)
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 Evolution of thymidylate synthasessynthases
GoalsGoals
1.1. Quantify and locate events of LGTQuantify and locate events of LGT
2.2. Find origins of each LGT event using Find origins of each LGT event using gene treesgene trees
3.3. When did Thy originate?When did Thy originate?
Studying Thy LGTStudying Thy LGT
Map ThyA and ThyX on the species treeMap ThyA and ThyX on the species tree Reconstruct Reconstruct ThyAThyA / / ThyXThyX / / bothboth at each at each
ancestorancestor
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:BLAST against ~400 whole genomes
How to reconstruct ?
Evolutionary models
Thy mapping on species tree
What are evolutionary What are evolutionary models useful formodels useful for??
XXA
AA
A
AA
X
A
Which one is more likely?
XXA
A
XA
AA
X
A
AAA+
XX
ThyX gain
A
ThyA loss
ThyX loss
A
ThyX gain, ThyA loss
Evolutionary modelsEvolutionary models
The aim of an evolutionary model: to describe The aim of an evolutionary model: to describe (often in probabilistic terms) the evolutionary (often in probabilistic terms) the evolutionary biological realitybiological reality
87.01.001.002.0
04.068.02.008.0
08.001.08.011.0
08.011.008.073.0
T
G
C
A
TGCA
LikelihoodLikelihood An evolutionary model enables us to An evolutionary model enables us to
compute the compute the likelihoodlikelihood that a certain that a certain scenario describes the biological reality we scenario describes the biological reality we observe.observe.
Learn the different probabilities from the Learn the different probabilities from the datadata
XXA
AA
A
AA
X
A
A+ X
XA
XXA
A
XA
AA
X
A
AA
A
A gain-loss evolutionary A gain-loss evolutionary modelmodel
4333
22
11
0
0
A
X
A+X
A X A+X
An evolutionary modelAn evolutionary model
4333
22
11
0
0
A
X
A+X
A X A+X
Rate of gain
Rate of loss
μ1, μ2, μ3, μ4 are maximum-likelihood estimates
ResultsResults
rate of rate of lossloss >> rate of >> rate of gaingain rate of gain ofrate of gain of ThyAThyA > gain of> gain of ThyXThyX
Results – Maximum Results – Maximum Likelihood ReconstructionLikelihood Reconstruction
At least:
14 LGT events where ThyA was swapped by ThyX (or vice versa)
Origin of Mycetozoa Origin of Mycetozoa ThyXThyX
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 Two possible explanationsexplanations
1.1. Mycetozoa eat bacteria Mycetozoa eat bacteria digested some bacterial DNAdigested some bacterial DNA
2.2. The ancestor of mitochondria The ancestor of mitochondria is known to be an is known to be an αα-proteobacteria -proteobacteria mitochondrial mitochondrial involvement?involvement?
VirusesViruses
Viral sequences’ distribution
Myoviridae
Siphoviridiae
Herpesviridae
Podoviridae
Early lifeEarly life
Beginning of life - RNA Beginning of life - RNA worldworld
“…“…The universal ancestor is not a discrete The universal ancestor is not a discrete entity. It is, rather, a diverse community of entity. It is, rather, a diverse community of cells that survives and evolves as a cells that survives and evolves as a biological unit…“ (Woese, 1998)biological unit…“ (Woese, 1998)
LGT
LUCA – the last universal common
ancestor, is a communal “swamp”
RNA RNA DNA world DNA world
Controversy around how DNA evolvedControversy around how DNA evolved
Archaea
Bacteria
Eukarya
Founder VirusesFounder Viruses
“…“…Viruses played a critical role in the Viruses played a critical role in the emergence of DNA…several independent emergence of DNA…several independent transfers [from viruses] produced the two cell transfers [from viruses] produced the two cell types (prokaryote/eukaryote) and the three types (prokaryote/eukaryote) and the three cellular domains …” (Forterre PNAS(103) 2006)cellular domains …” (Forterre PNAS(103) 2006)
Archaea
Bacteria
Eukarya
virus
Viruses and Thy in early lifeViruses and Thy in early life
ThyA gene tree
T4 like phages
T4 like phages hosts
ThyA gene treeThyA gene tree
Bacteria(hosts)
Eukarya
T4-like phages
Archaea
?
A model for Thy evolution in A model for Thy evolution in early lifeearly life
LGT
RNA world and RNA RNA world and RNA virusesviruses
Viruses modify their Viruses modify their genome to evade host genome to evade host
defensedefense
Thymidine
Thymidylate synthase
Thymidine
dCMP dCMP hydroxymethylase hydroxymethylase ))CHCH((
In fact – T4 like phages use a similar tactic In fact – T4 like phages use a similar tactic today!today!
Hydroxy-methylated cytosine
CH
Thymidine
Interestingly, CH and ThyA are homologs Interestingly, CH and ThyA are homologs (sequentially and structurally)(sequentially and structurally)
Song et al. EMBO J (18) 1999
SummarySummary
Open questions:
When did ThyX come in and how?
Who predated who?
Why is there so much LGT between these two enzymes?ThyA
Thank youThank you.… .… Dr. Tal PupkoDr. Tal Pupko Shaul Shaul, Itay MayroseShaul Shaul, Itay Mayrose Dr. Uri GophnaDr. Uri Gophna
Lab members:Lab members:Adi DoronAdi DoronEyal PrivmanEyal PrivmanNimrod RubinsteinNimrod RubinsteinOsnat PennOsnat PennDudu BursteinDudu BursteinOfir CohenOfir Cohen