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.

3) Genetic code is unified because of natural selection for unity per se – i.e. horizontal gene transfer is essential to evolution itself.

Possible explanations for the unity of the genetic code entertained by Crick

But there was a third possible explanation

0.1

Metcoc jaAquifex

Thermot ma

CAUCR

Ecoli

Chlamy trChloro te

B.subtilusSynecococ

Strep coe

Haloba maMetsar ma

Thermo ac

Archae fu

Metpyr kaMetthe th

Pyroco-ab

Pyrobac aeAeropyrum

Sulfolobus

Plasmodium

Yeast

NeurosporaC.elegansHuman

CatfishRice

Ribosomal protein tree

eukaryote

archaea

gram (-)

gram (+)

eukaryote archaea

gram (-) gram (+)

eukaryote

archaea

gram (-)

gram (+)

Tree 1

Tree 3

Tree 2

Quartet partitions

What was found was support for NONE of the three trees, instead:

eukaryote

archaea

gram (-)

gram (+)

Star phylogeny

18 of the 26 homologue submitted to the quartet analysisdisplayed the star phylogeny. They include:

argD ornithine carbamoyl transferaseargT arginine tRNA synthetase argH arginine biosynthesistrpA tryptophan synthetase αtrpB tryptophan synthetase βmutS,H mismatched DNA repairpurA purine biosynthesispurB “pur5 “pur6 “

0.1

Metcoc jaAquifex

Thermot ma

CAUCR

Ecoli

Chlamy trChloro te

B.subtilusSynecococ

Strep coe

Haloba maMetsar ma

Thermo ac

Archae fu

Metpyr kaMetthe th

Pyroco-ab

Pyrobac aeAeropyrum

Sulfolobus

Plasmodium

Yeast

NeurosporaC.elegansHuman

CatfishRice

Ribosomal protein tree

0.1

Neurospora

C.elegans

sch pombeYeast

Drosophila

Human

Zebrafish

themoc ac

metcoc jasynecoc

metsar ma

pyrococ abCAUCR

thermo ma

E.coli

Streptomyc

aeropyrum

pyrobac

B.subtilismetthe th

aquifex

metpyr ka

halobacterchlorobium

riceArabidopsi

Ornithine carbamoyl transferaseBifurcated tree

0.1

Neurospora

C.elegans

sch pombeYeast

Drosophila

Human

Zebrafish

themoc ac

metcoc jasynecoc

metsar ma

pyrococ abCAUCR

thermo maE.coli

Streptomyc

aeropyrum

pyrobac

B.subtilismetthe th

aquifex

metpyr ka

halobacterchlorobium

rice

Arabidopsi

Ornithine carbamoyl transferaseColapse unsupported bifurcations

0.1

Archaeog

haloferax

Methanolob

Methanosarthet

thermus

legionel

zymonas

CaucreRhodomic

Pseudomo

bacillisE.coli

buchnera

AcanthamGuillardtrametescoprinusneucra

nodulispcandida

spathospHalobacteClostrid

Nostoc

arabidopsioryza

Trptophan synthase (α and β)Bifurcated tree

0.1

Archaeog

haloferax

MethanolobMethanosar

thet

thermus

legionel

zymonas

CaucreRhodomic

Pseudomobacillis

E.coli

buchnera

AcanthamGuillardtrametescoprinusneucra

nodulisp candidaspathospHalobacteClostrid

Nostoc

arabidopsioryza

Trptophan synthase (α and β)Collapse bifurcations

0.1

HumanMt

Neurospora

YeastSch.pombe

E.coli

CAUCR

Strep coe

OrzyaSynecococ

Chlamy tr

Plasmodium

D.melanogaC.elegans

Zebra fish Human

Pyroco-ab

Pyrobac ae

Aeropyrum

sulfolobusArchae fu

Thermo ac

Chlorobium

Thermot ma

B.subtilis

Aguifex

Haloba maMetpyr kaMetcoc jaMetthe th

Metsar ma

Arginine-tRNA ligase

Tryptophan-tRNA Ligase

0.1

Yeaststrmy co

E.col

B.subtilis

C.eleganssynecoc

CAUCR

chlamy trChlorobium

Aquifexthermot ma

metcoc jametpyr ka

thermo ac

methe thAeropyrum

archae fu

haloba su2metsar ma

pyrobac aepyroco ab

sulfolobusPlasmodium

haloba su1

schizopNeurospora

Rice

Human

0.1

ecolimetbar

thermmar

halmarnatrpha

clotet

strpnebacanthcaucre

dictyostecelegans

plafal

saccer

drosophila

cionaseaurchin

gallus

schpom arabidopsineucra

zfishmousehuman

oryza

MutS protein family

Distance ACTase

DistanceOCTase

1 E.coli/Salmonella; Pea/arabidopsis2 E.coli/Haemophilis; Yeast/neurospora3 Plants/metazoa; plants/ fungi

Whole matrix rate test comparingOrnithine carbamoyl and Aspartate carbamoyl

Transferases

Whole matrix rate test comparingTryptophan 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 proteinchemistry 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 thethe entire genetic code evolved within multiple demes that are linked together byHorizontal 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

Bacteria Ytl

Ytl + Wtl

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