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Molecular evolution before the ancestors of the
bacterial and archaeal domains and before the Last
Universal Common Ancest...
Outline:
MuralatNASAAmesResearchCenter
•  Gene	
  duplica,ons	
  and	
  deep	
  molecular	
  phylogenies	
  
•  Proper,es	...
Catalytic subunits Non catalytic subunits
speciation
gene duplication
time
ATPase	
  /	
  ATPsynthase	
  	
  
	
  ATP	
  binding	
  Subunits	
  
N C
V-proteolipid
N
CN C
A-proteolipids
Halobacterium Methanococcus
β	

α	

 α	

β	

c
A
B
A
A
B
B
c
N C
F-proteolipid
V-t...
?
mesophilicthermophilic
Archaea Eukarya Bacteria
endosymbionts
1
2
3
4
5
A
B
C
D E
12	
  proteolipid	
  Ds	
  /	
  6	
  c...
 
	
  
C.	
  R.	
  Woese	
  and	
  G.	
  E.	
  Fox	
  (1977)	
  J.	
  Mol.	
  Evol.	
  10,	
  1-­‐6:	
  
	
  
“Eucaryotes	...
According	
  to	
  Woese	
  and	
  Fox	
   According	
  to	
  V/F/A-­‐ATPases	
  
From:	
  
GOGARTEN	
  J.P.,	
  OLENDZENS...
In	
  R.P.	
  Mortlock:	
  (ed),	
  The	
  Evolu,on	
  of	
  Metabolic	
  Func,on	
  ,	
  CRC	
  Press,1992	
  	
  
Organisms	
  represented	
  by	
  the	
  root	
  of	
  the	
  universal	
  evolu,onary	
  tree	
  were	
  	
  
most	
  lik...
Outline:
MuralatNASAAmesResearchCenter
•  Gene	
  duplica,ons	
  and	
  deep	
  molecular	
  phylogenies	
  
•  Proper,es	...
A Radical Proposal by Eugene Koonin :
Anthropic Chemical Evolution
(The Logic of Chance – FT Press 2012)
•  Modern cosmolo...
These	
  hypotheses	
  can	
  be	
  tested	
  by	
  
examining	
  the	
  composi,on	
  of	
  
reconstructed	
  ancestor	
 ...
Hypothesis Testing
1-2: neofunctionalization
3: subfunctionalization
4: takeover (parafunctionalization)
Probability densi...
Results
• Majority of high-probabilitiy
positions are resolved for Ile or Val
• Supports both amino acids are
specifically...
"RNA	
  –	
  world"	
  
(single	
  biopolymer	
  world)	
  
Replica,on	
  Machinery	
  	
  
"RNA	
  –	
  world"	
  
(single	
  biopolymer	
  world)	
  
Replica,on	
  Machinery	
  	
  
Rise	
  of	
  protein	
  as	
 ...
"RNA	
  –	
  world"	
  
(single	
  biopolymer	
  world)	
  
Replica,on	
  Machinery	
  	
  
Rise	
  of	
  protein	
  as	
 ...
"RNA	
  –	
  world"	
  
(single	
  biopolymer	
  world)	
  
Replica,on	
  Machinery	
  	
  
Rise	
  of	
  protein	
  as	
 ...
"RNA	
  –	
  world"	
  
(single	
  biopolymer	
  world)	
  
Replica,on	
  Machinery	
  	
  
Rise	
  of	
  protein	
  as	
 ...
Conclusions 1st part
•  Extrapolation of ATPsynthase structure suggests that
LUCA was able to use transmembrane ion gradie...
Outline:
MuralatNASAAmesResearchCenter
•  Gene	
  duplica,ons	
  and	
  deep	
  molecular	
  phylogenies	
  
•  Proper,es	...
Evolution of the Ribosome
•  “Core” of ribosome consists of RNA +
subset of ribosomal proteins universally
conserved in al...
Compositional Stratigraphy
“We perform a compositional analysis of ribosomal proteins and ATPase
subunits in bacterial and...
Roo,ng	
  the	
  Ribosomal	
  Tree	
  of	
  Life	
  using	
  an	
  Echo	
  from	
  the	
  Early	
  Expansion	
  of	
  the	...
Fig.	
  3.	
  The	
  classical	
  SSUrRNA	
  distance	
  tree,	
  presented	
  as	
  rooted	
  in	
  the	
  bacterial	
  b...
LUCA (located on the “bacterial branch”) was less
thermophilic than the ancestor of the bacterial and
archaeal domains
•  ...
Gogarten issol2014 version4
Gogarten issol2014 version4
Gogarten issol2014 version4
Gogarten issol2014 version4
Gogarten issol2014 version4
Gogarten issol2014 version4
Gogarten issol2014 version4
Gogarten issol2014 version4
Gogarten issol2014 version4
Gogarten issol2014 version4
Gogarten issol2014 version4
Gogarten issol2014 version4
Gogarten issol2014 version4
Gogarten issol2014 version4
Gogarten issol2014 version4
Gogarten issol2014 version4
Gogarten issol2014 version4
Gogarten issol2014 version4
Gogarten issol2014 version4
Gogarten issol2014 version4
Gogarten issol2014 version4
Gogarten issol2014 version4
Gogarten issol2014 version4
Gogarten issol2014 version4
Gogarten issol2014 version4
Gogarten issol2014 version4
Gogarten issol2014 version4
Gogarten issol2014 version4
Gogarten issol2014 version4
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Gogarten issol2014 version4

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Gogarten issol2014 version4

  1. 1. Molecular evolution before the ancestors of the bacterial and archaeal domains and before the Last Universal Common Ancestor Funded through the NASA Exobiology and NSF Assembling the Tree of Life Programs Origins 2014, Nara, Japan, July 6-11, 2014 J. Peter Gogarten University of Connecticut Dept. of Molecular and Cell Biol. Collaborators: Dr. Greg Fournier (UConn/MIT) Dr. Cheryl Andam (UConn/Harvard)
  2. 2. Outline: MuralatNASAAmesResearchCenter •  Gene  duplica,ons  and  deep  molecular  phylogenies   •  Proper,es  of  the  Last  Universal  Common  Ancestor(s)   •  The  history  of  the  transla,on  machinery  during  the  expansion  of  the   gene,c  code   •  The  ribosomal  tree  of  life  and  inferred  op,mal  growth  temperature     •  Tree  shape,  the  ar,fact  of  apparent  “lonely  ancestors”     •  Indica,ons  for  early  ex,nc,on  events  due  to  increased  environmental   temperature   •  Phylogene,c  evidence  for  LUCA’s  compatriots    
  3. 3. Catalytic subunits Non catalytic subunits speciation gene duplication time
  4. 4. ATPase  /  ATPsynthase      ATP  binding  Subunits  
  5. 5. N C V-proteolipid N CN C A-proteolipids Halobacterium Methanococcus β α α β c A B A A B B c N C F-proteolipid V-type ATPase A-type ATPase F-type ATPase α β Methanopyrus
  6. 6. ? mesophilicthermophilic Archaea Eukarya Bacteria endosymbionts 1 2 3 4 5 A B C D E 12  proteolipid  Ds  /  6  cataly,c  SU  =                                  2  H+(Na+)  /  ATP   12  proteolipid  Ds  /  3  cataly,c  SU  =                                4H+(Na+)  /  ATP   6  proteolipid  Ds  /  3  cataly,c  SU  =                                2H+(Na+)  /  ATP   12  proteolipid  Ds  /  3  cataly,c  SU  =                                4H+(Na+)  /  ATP   12  proteolipid  Ds  /  3  cataly,c  SU  =                                4H+(Na+)  /  ATP   Reversible  Enzyme     Reversible  Enzyme    Dedicated  Ion  Pump   Dedicated  Ion  Pump   Reversible  Enzyme    
  7. 7.     C.  R.  Woese  and  G.  E.  Fox  (1977)  J.  Mol.  Evol.  10,  1-­‐6:     “Eucaryotes  did  arise  from  procaryotes,  but  only  in  the  sense   that  the  procaryo6c  is  an  organiza6onal,  not  a  phylogene6c   dis6nc6on.  In  analogous  fashion  procaryotes  arose  from   simpler  en66es.  The  la<er  are  properly  called  progenotes,   because  they  are  s6ll  in  the  process  of  evolving  the   rela6onship  between  genotype  and  phenotype.”    
  8. 8. According  to  Woese  and  Fox   According  to  V/F/A-­‐ATPases   From:   GOGARTEN  J.P.,  OLENDZENSKI  L.,  (1999)  The  Progenote,     Encyclopedia  of  Molecular  Biology,  Thomas  Creighton,  ed.,   John  Wiley  and  Sons,  NY  (submieed  version  at  gogarten.uconn.edu)  
  9. 9. In  R.P.  Mortlock:  (ed),  The  Evolu,on  of  Metabolic  Func,on  ,  CRC  Press,1992    
  10. 10. Organisms  represented  by  the  root  of  the  universal  evolu,onary  tree  were     most  likely  complex  cells  with  a  sophis,cated  protein  transla,on  system  and   a  DNA  genome  encoding  hundreds  of  genes.    
  11. 11. Outline: MuralatNASAAmesResearchCenter •  Gene  duplica,ons  and  deep  molecular  phylogenies   •  Proper,es  of  the  Last  Universal  Common  Ancestor(s)   •  The  history  of  the  transla:on  machinery  during  the  expansion  of  the   gene:c  code   •  The  ribosomal  tree  of  life  and  inferred  op,mal  growth  temperature     •  Tree  shape,  the  ar,fact  of  apparent  “lonely  ancestors”     •  Indica,ons  for  early  ex,nc,on  events  due  to  increased  environmental   temperature   •  Phylogene,c  evidence  for  LUCA’s  compatriots    
  12. 12. A Radical Proposal by Eugene Koonin : Anthropic Chemical Evolution (The Logic of Chance – FT Press 2012) •  Modern cosmologies postulate parallel worlds, for example assuming an eternal inflation period, resulting in an infinite number of universes (Villinkin, 2007). •  Given an infinite number of universes, even unlikely events are bound to happen in some universes (and because we are made from two biopolymers, we are in one of the universes where this rare event occurred). •  Koonin suggests that the assembly of the translation machinery is a candidate for such an unlikely event. •  Finding exceedingly rare events in evolution would argue for a Multi World Cosmology.
  13. 13. These  hypotheses  can  be  tested  by   examining  the  composi,on  of   reconstructed  ancestor  sequences   Do  synthetase  paralogs  retain  evidence   of  pre-­‐LUCA  evolu,onary  events?  
  14. 14. Hypothesis Testing 1-2: neofunctionalization 3: subfunctionalization 4: takeover (parafunctionalization) Probability density graph of all positions with X+Y plurality consensus in ancestral reconstruction of cognate paralog ancestor.
  15. 15. Results • Majority of high-probabilitiy positions are resolved for Ile or Val • Supports both amino acids are specifically encoded at the time of the paralog ancestor, Parafunctionalization • Large number of nondiscriminating positions between Ile and Val would support subfunctionalization • However, these positions are all low-probability, and match with the control simulation, so probably artifact of poorly conserved positions.
  16. 16. "RNA  –  world"   (single  biopolymer  world)   Replica,on  Machinery    
  17. 17. "RNA  –  world"   (single  biopolymer  world)   Replica,on  Machinery     Rise  of  protein  as  second  biopolymer   tRNAs,  "RNA"  Ribosome,     RNA  based  tRNA  charging  mechanisms  
  18. 18. "RNA  –  world"   (single  biopolymer  world)   Replica,on  Machinery     Rise  of  protein  as  second  biopolymer   tRNAs,  "RNA"  Ribosome,     RNA  based  tRNA  charging  mechanisms   Expansion  of  the  gene,c  code  to   include  Isoleucine  and  Valine  
  19. 19. "RNA  –  world"   (single  biopolymer  world)   Replica,on  Machinery     Rise  of  protein  as  second  biopolymer   tRNAs,  "RNA"  Ribosome,     RNA  based  tRNA  charging  mechanisms   Expansion  of  the  gene,c  code  to   include  Isoleucine  and  Valine   Takeover  of  charging  mechanism   by  proteins  (inven,on  of     aminoacyl  tRNA  synthetases)   1IVS.pdb  valRS  +  tRNAval    
  20. 20. "RNA  –  world"   (single  biopolymer  world)   Replica,on  Machinery     Rise  of  protein  as  second  biopolymer   tRNAs,  "RNA"  Ribosome,     RNA  based  tRNA  charging  mechanisms   Expansion  of  the  gene,c  code  to   include  Isoleucine  and  Valine   Takeover  of  charging  mechanism   by  proteins  (inven,on  of     aminoacyl  tRNA  synthetases)   Expansion  of  the  gene,c  code  to   include  Tryptophan   1IVS.pdb  valRS  +  tRNAval    
  21. 21. Conclusions 1st part •  Extrapolation of ATPsynthase structure suggests that LUCA was able to use transmembrane ion gradients to synthesize ATP. •  LUCA was not a progenote •  The expansion of the genetic code did not parallel the divergence of aaRSs; rather aaRS acquired specificity in cells that were already able to charge tRNAs with their cognate aa through other means (likely exception tryptophan).
  22. 22. Outline: MuralatNASAAmesResearchCenter •  Gene  duplica,ons  and  deep  molecular  phylogenies   •  Proper,es  of  the  Last  Universal  Common  Ancestor(s)   •  The  history  of  the  transla,on  machinery  during  the  expansion  of  the   gene,c  code   •  The  ribosomal  tree  of  life  and  inferred  op:mal  growth  temperature     •  Tree  shape,  the  ar,fact  of  apparent  “lonely  ancestors”     •  Indica,ons  for  early  ex,nc,on  events  due  to  increased  environmental   temperature   •  Phylogene,c  evidence  for  LUCA’s  compatriots    
  23. 23. Evolution of the Ribosome •  “Core” of ribosome consists of RNA + subset of ribosomal proteins universally conserved in all life (~29 proteins) (Harris et al., 2003) •  Likely coevolved with genetic code within an RNA world (Wolf & Koonin, 2007)
  24. 24. Compositional Stratigraphy “We perform a compositional analysis of ribosomal proteins and ATPase subunits in bacterial and archaeal lineages, using conserved positions that came and remained under purifying selection before and up to the most recent common ancestor. An observable shift in amino acid usage at these conserved positions likely provides an untapped window into the history of protein sequence space, allowing events of genetic code expansion to be identified.” Fournier GP, Gogarten JP. 2007. Signature of a primitive genetic code in ancient protein lineages. J Mol Evol. 65(4):425-436
  25. 25. Roo,ng  the  Ribosomal  Tree  of  Life  using  an  Echo  from  the  Early  Expansion  of  the  Gene,c  Code   (Fournier and Gogarten, MBE 2010)
  26. 26. Fig.  3.  The  classical  SSUrRNA  distance  tree,  presented  as  rooted  in  the  bacterial  branch.   Bold  lines  indicate  extreme  hyperthermophiles.  From  Steeer  (1996).  
  27. 27. LUCA (located on the “bacterial branch”) was less thermophilic than the ancestor of the bacterial and archaeal domains •  Boussau, B, Blanquart, S, Necsulea, A, Lartillot, N and Gouy, M (2008). Parallel adaptations to high temperatures in the Archaean eon. Nature 456(7224): 942-945

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