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Transcript
Possible explanations for the unity of the genetic code
entertained by Crick
1) Frozen-accident – once the complete code was formed this defined the universal
common ancestor from which all life evolved.
2) Steric constraint - The current code is functionally constrained because
because of a chemical fit between codon and amino acid.
Possible explanations for the unity of the genetic code
entertained by Crick
1) Frozen-accident – once the complete code evolved this defined the universal
common ancestor from which to all life evolved.
2) Steric constraint - The current code is functionally constrained because
because of a chemical fit between codon and amino acid.
But there was a third possible explanation
3) Genetic code is unified because of natural selection for unity per se
– i.e. horizontal gene transfer is essential to evolution itself.
Ribosomal protein tree
Yeast
Sulfolobus
Aeropyrum
Pyrobac ae
Plasmodium
Neurospora
C.elegans
Human
Catfish
Rice
Pyroco-ab
Metthe th
Metpyr ka
Archae fu
Aquifex
Metcoc ja
Thermo ac
Thermot ma
Metsar ma
Haloba ma
CAUCR
Strep coe
0.1
Ecoli
B.subtilus
Synecococ
Chloro te
Chlamy tr
Quartet partitions
gram (+)
archaea
Tree 1
gram (-)
eukaryote
eukaryote
archaea
Tree 2
gram (-)
gram (+)
archaea
gram (+)
gram (-)
eukaryote
Tree 3
What was found was support for NONE of the three trees,
instead:
gram (+)
archaea
gram (-)
eukaryote
Star phylogeny
18 of the 26 homologue submitted to the quartet analysis
displayed the star phylogeny. They include:
argD
argT
argH
trpA
trpB
mutS,H
purA
purB
pur5
pur6
ornithine carbamoyl transferase
arginine tRNA synthetase
arginine biosynthesis
tryptophan synthetase α
tryptophan synthetase β
mismatched DNA repair
purine biosynthesis
“
“
“
Ribosomal protein tree
Yeast
Sulfolobus
Aeropyrum
Pyrobac ae
Plasmodium
Neurospora
C.elegans
Human
Catfish
Rice
Pyroco-ab
Metthe th
Metpyr ka
Archae fu
Aquifex
Metcoc ja
Thermo ac
Thermot ma
Metsar ma
Haloba ma
CAUCR
Strep coe
0.1
Ecoli
B.subtilus
Synecococ
Chloro te
Chlamy tr
Ornithine carbamoyl transferase
Bifurcated tree
Streptomyc
pyrobac
aquifex
aeropyrumB.subtilis
metthe th metpyr ka
halobacter
thermo ma
chlorobium
E.coli
CAUCR
pyrococ ab
metsar ma
synecoc
rice
Arabidopsi
Neurospora
themoc ac
metcoc ja
C.elegans
Zebrafish
Human
0.1
Drosophila
sch pombe
Yeast
Ornithine carbamoyl transferase
Colapse unsupported bifurcations
pyrobac
Streptomyc
aquifex
aeropyrumB.subtilis
metthe th metpyr ka
E.coli
halobacter
thermo ma
chlorobium
CAUCR
pyrococ ab
Arabidopsi
metsar ma
synecoc
rice
Neurospora
themoc ac
metcoc ja
C.elegans
Zebrafish
Human
0.1
Drosophila
sch pombe
Yeast
Trptophan synthase (α and β)
Bifurcated tree
candida
nodulisp
spathosp
neucra
Halobacte
coprinus
Clostrid
trametes
arabidopsi
Guillard
oryza
Nostoc
Acantham
haloferax
buchnera
Methanolob
E.coli
bacillis
thet
Methanosar
Archaeog
legionel
Pseudomo
0.1
Rhodomic
Caucre
thermus
zymonas
Trptophan synthase (α and β)
Collapse bifurcations
nodulisp candida
spathosp
neucra
Halobacte
coprinus
Clostrid
trametes
arabidopsi
Guillard
oryza
Nostoc haloferax
Acantham
buchnera
Methanolob
thet
E.coli Archaeog
Methanosar
bacillis
legionel
Pseudomo
Rhodomic
0.1
Caucre
thermus
zymonas
Arginine-tRNA ligase
Chlorobium
Thermot ma
Thermo ac
sulfolobusArchae fu
Aeropyrum
Pyrobac ae
Pyroco-ab
B.subtilis
Aguifex
Haloba ma
Metpyr ka
Metcoc ja
Metthe th
Metsar ma
Zebra fish Human
C.elegans
D.melanoga
Plasmodium
Chlamy tr
Synecococ Orzya
HumanMt
Neurospora
E.coli
Strep coe
0.1
CAUCR
Yeast
Sch.pombe
Tryptophan-tRNA Ligase
haloba su1
Plasmodium
sulfolobus
pyroco ab
pyrobac ae
metsar ma
haloba su2
archae fu
Aeropyrum
methe th
metcoc ja
metpyr ka
Neurospora
schizop
Rice
Human
Yeast
strmy co
E.col
thermo ac
B.subtilis
C.elegans
synecoc
CAUCR
0.1
thermot ma
Aquifex
chlamy tr
Chlorobium
MutS protein family
schpom
seaurchin
gallus
ciona
arabidopsi
neucra
zfish
mouse
human
drosophila
saccer
oryza
ecoli
metbar
thermmar
plafal
celegans
dictyoste
halmar
clotet
caucre
natrpha
bacanthstrpne
0.1
Whole matrix rate test comparing
Ornithine carbamoyl and Aspartate carbamoyl
Transferases
Distance
OCTase
Distance ACTase
1 E.coli/Salmonella; Pea/arabidopsis
2 E.coli/Haemophilis; Yeast/neurospora
3 Plants/metazoa; plants/ fungi
Whole matrix rate test comparing
Tryptophan synthetase and
Aspartate carbamoylTransferases
Distance
trpA
Distance ACTase
I have shown that the evolution for multiple genes in the tryptophan and arginine
biosynthetic pathways, as well as their tRNA ligases show unusual phylogenies.
If we discard functional constraint arguments (i.e. that some kind of peculiar protein
chemistry is driving their evolution) then we can offer the following interpretation:
These genes “found in the three kingdoms that are not just unusually highly conserved
but whose topologies, when deduced from their sequences, strongly suggest that
they evolved after Archaea, Bacteria and Eukaryotes had already diversified.
In other words, these universal genes appear to be younger than the taxonomic
groups in which they are found today “
That is to say, there was a time when Archaea, Bacteria and Eukaryotes existed but that
they lacked the amino acids arginine and tryptophan.
If so, then LUCA, if it ever existed, could not have had those two amino acids. Thus the
current universal distribution of arginine and tryptophan is not explained by LUCA. Once
we start down this road of reasoning there is no reason why we cannot imagine the
the entire genetic code evolved within multiple demes that are linked together by
Horizontal gene transfer.
Possible outline for the emergence of
tryptophan (W) tRNA ligase by duplication
and horizontal spread of tyrosine (Y) tRNA ligase
??
Archaea
Ytl
??
Eukarya
Ytl
Ytl
Ytl + Wtl
??
Bacteria
Ytl
Ytl
Ytl + Wtl
Ytl + Wtl
Ytl + Wtl
Xianchi Dong, Minyun Zhou, Chen Zhong1, Bei Yang, Ning Shen and Jianping Ding
(2010) “Crystal structure of Pyrococcus horikoshiitryptophanyl-tRNA synthetase
and structure-based phylogenetic analysis suggest an archaeal origin of
tryptophanyl-tRNA synthetase”
Nucleic Acids Research Volume 38, . 1401-1412
“Our results raise the possibility that
present day tyrosyl- and tryptophanyl-tRNA
synthetases appeared after the separation of
nucleated cells from eubacteria.”
Darwin’s notion of the Tree of Life
“There is grandeur in this view of life, with its
several powers, having been originally breathed
into a few forms or into one; and that, whilst this
planet has gone cycling on according to the fixed
law of gravity, from so simple a beginning endless
forms most beautiful and most wonderful have been,
and are being, evolved.”
― Charles Darwin, The Origin of Species