presentation at origins 2014

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. 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. Catalytic subunits Non catalytic subunits
speciation
gene duplication
time

4. ATPase
/
ATPsynthase
ATP
binding
Subunits

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. ?
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.
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. 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. In
R.P.
Mortlock:
(ed),
The
Evolu,on
of
Metabolic
Func,on
,
CRC
Press,1992

11. 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.

12. 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

13. 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.

14. 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?

15. 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.

16. 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.

17. "RNA
–
world"
(single
biopolymer
world)
Replica,on
Machinery

18. "RNA
–
world"
(single
biopolymer
world)
Replica,on
Machinery
Rise
of
protein
as
second
biopolymer
tRNAs,
"RNA"
Ribosome,
RNA
based
tRNA
charging
mechanisms

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

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)
1IVS.pdb
valRS
+
tRNAval

21. "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

22. 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).

23. 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

24. 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)

25. 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

26. Roo,ng
the
Ribosomal
Tree
of
Life
using
an
Echo
from
the
Early
Expansion
of
the
Gene,c
Code
(Fournier and Gogarten, MBE 2010)

27. Fig.
3.
The
classical
SSUrRNA
distance
tree,
presented
as
rooted
in
the
bacterial
branch.
Bold
lines
indicate
extreme
hyperthermophiles.
From
Steeer
(1996).

28. 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
Reconstruction of ancestral protein and rRNA sequences
Based on IVYWREL and rRNA stem G+C content LUCA was
less thermophilic than the domain ancestors.
• Galtier, N, Tourasse, N and Gouy, M (1999). A
nonhyperthermophilic common ancestor to extant life forms.
Science 283(5399): 220-221.8
• rRNA 60°C!80°C
IVYWREL (corrected for GC content) 20°C!70°C

29. 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

30. Tree, Web, or Coral of Life?
Charles Darwin
painted by George Richmond in
the late 1830
Page B26 from Charles Darwin’s (1809-1882)
notebook (1837/38)
“The tree of life should perhaps be called
the coral of life, base of branches dead”

31. The Coral of Life (Darwin)
ZHAXYBAYEVAandGOGARTEN(2004):
Cladogenesis,CoalescenceandtheEvolutionoftheThreeDomainsofLife.
TrendsinGenetics20(4):182-187

32. The Coral of Life (Darwin)
ZHAXYBAYEVAandGOGARTEN(2004):
Cladogenesis,CoalescenceandtheEvolutionoftheThreeDomainsofLife.
TrendsinGenetics20(4):182-187

33. Coalescence
–
the
process
of
tracing
lineages
backwards
in
,me
to
their
common
ancestors.
Every
two
extant
lineages
coalesce
to
their
most
recent
common
ancestor.
Eventually,
all
lineages
coalesce
to
the
cenancestor.
t/2
(Kingman,
1982)
Illustra,on
is
from
J.
Felsenstein,
“Inferring
Phylogenies”,
Sinauer,
2003

34. EXTANT
LINEAGES
FOR
THE
SIMULATIONS
OF
50
LINEAGES

35. Bacterial
16SrRNA
based
phylogeny
(from
P.
D.
Schloss
and
J.
Handelsman,
Microbiology
and
Molecular
Biology
Reviews,
December
2004.)
The
devia,on
from
the
“long
branches
at
the
base”
paeern
could
be
due
to
•
under
sampling
•
an
actual
radia,on
•
due
to
an
inven,on
that
was
not
transferred
•
following
a
mass
ex,nc,on

36. Near
frustra,on
of
early
life
From:
Gogarten-­‐Boekels
M,
Hilario
E,
Gogarten
JP.
Orig
Life
Evol
Biosph.
1995
Jun;25(1-­‐3):
251-­‐64.
The
effects
of
heavy
meteorite
bombardment
on
the
early
evolu:on
—the
emergence
of
the
three
domains
of
life.

37. From:
hep://www.origin-­‐life.gr.jp/3603/3603055/3603055.html
Alterna,ve:
tail
of
early
heavy
bombardment
–
Nicolle
Zellner’s
talk
on
Tuesday
See
Marchi
et
al.
Nature
2014
for
a
recent
update.

38. 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

39. Molecular
Phylogenies
Lonely
Ancestors
From:
hep://itol.embl.de/
iTol
The
interac,ve
Tree
of
Life
Ciccarelli
et
al,
Science.
2006
311
:1283-­‐7
• Tree
topology
averaged
over
many
genes
(mainly
ribosomal
proteins).
• No
re,cula,ons.
• Branches
do
not
reflect
,me.
• Only
extant
organisms
and
their
lucky
ancestors
are
includes
Noteworthy:

40. The Coral of Life (Darwin)
ZHAXYBAYEVAandGOGARTEN(2004):
Cladogenesis,CoalescenceandtheEvolutionoftheThreeDomainsofLife.
TrendsinGenetics20(4):182-187

41. The Coral of Life (Darwin)
ZHAXYBAYEVAandGOGARTEN(2004):
Cladogenesis,CoalescenceandtheEvolutionoftheThreeDomainsofLife.
TrendsinGenetics20(4):182-187

42. Molecular
phylogenies
of
aaRSs
reveal
other
lineages
that
coexisted
with
LUCA
and/or
the
domain
ancestors
and
transferred
some
of
their
genes
into
extant
lineages.

43. Pyrrolysine (Pyl)
# 22nd genetically encoded amino acid to be discovered
# Uses dedicated aminoacyl-tRNA synthetase (PylS) and a UAG-recognizing tRNA.
# Found only within Methanosarcinae, Desulfitobacterium hafniense and a single
marine worm symbiont delta-proteobacteria.
# Used exclusively at the catalytic site of three enzymes responsible for the initial step
of methylotrophic methanogenesis from methylamines.
MtmB structure with Pyl residue in catalytic core (Hao
et al., 2002)
Synthesized from Pro and Lys
Contains a peptide bond in the side chain

44. Class II aaRS Phylogeny
LUCA -nodes

45. Horizontal Gene Transfer
● Pyl evolved and had a pervasive biological role in an ancient sister group to the
MRCA.
● Transfer of cassette encoding methyltransferases and pyrrolysine system, selected for
by the transfer of the methyltransferase genes.
● Subsequent extinction of the entire donor lineage
Genetic Life Raft

46. Ancient
origin
of
the
divergent
forms
of
leucyl-­‐tRNA
synthetases
in
the
Halobacteriales
Cheryl
P
Andam,
Timothy
J
Harlow,
R
Thane
Papke
and
J
Peter
Gogarten
BMC
Evolu6onary
Biology
12:85
leucyl-tRNA synthetase
(class I) phylogeny

47. Homeoalleles
• Variants that have the same general function,
but can have distinct characteristics.
• Gene pool contains different homeoalleles, but
individual strains and species usually contain
only one of the alleles.
• Can be brought together temporarily in a
lineage through HGT
Andam, Williams, Gogarten 2010 PNAS

48. Andam
and
Gogarten
2011

49. Phylogeny of selected class II amino acyl tRNA synthetases

50. Andam
and
Gogarten
2011
Distribu:on
of
rare
SerRS
in
Archaea

51. thrRS and serRS phylogeny
Eukaryotes
Euryachaeota
Crenarchaeota
Bacteria
Alignment
with
PRANK
and
SATé,
tree
with
phyml
(WAG,
gamma
+I)

52. Conclusion 2nd part
• Tree shape and amino acid composition of
ancestral sequences suggest a bottleneck
due to increased environmental temperature
at the base of the bacterial and archaeal
domains.
• Studies of horizontal gene transfers of
aaRSs suggest that more than two lineages
passed through this bottleneck.

54. References
• Andam
CP,
Gogarten
JP.
2011.
Biased
gene
transfer
in
microbial
evolu,on.
Nat.
Rev.
Microbiol.
9:543–555.
• Andam
CP,
Harlow
TJ,
Papke
RT,
Gogarten
JP.
2012.
Ancient
origin
of
the
divergent
forms
of
leucyl-­‐tRNA
synthetases
in
the
Halobacteriales.
BMC
Evol.
Biol.
12:85.
• Andam
CP,
Williams
D,
Gogarten
JP.
2010.
Biased
gene
transfer
mimics
paeerns
created
through
shared
ancestry.
Proc.
Natl.
Acad.
Sci.
U.
S.
A.
107:10679–10684.
• Boussau
B,
Blanquart
S,
Necsulea
A,
Lar,llot
N,
Gouy
M.
2008.
Parallel
adapta,ons
to
high
temperatures
in
the
Archaean
eon.
Nature
456:942–945.
• Ciccarelli
FD,
Doerks
T,
von
Mering
C,
Creevey
CJ,
Snel
B,
Bork
P.
2006.
Toward
automa,c
reconstruc,on
of
a
highly
resolved
tree
of
life.
Science
311:1283–1287.
• Delaye
L,
Becerra
A,
Lazcano
A.
2005.
The
last
common
ancestor:
what’s
in
a
name?
Orig
Life
Evol
Biosph
35:537–554.
• Felsenstein
J.
2003.
Inferring
Phylogenies.
Sinauer,
Sunderland,
MA
• Fournier
GP,
Andam
CP,
Alm
EJ,
Gogarten
JP.
2011.
Molecular
evolu,on
of
aminoacyl
tRNA
synthetase
proteins
in
the
early
history
of
life.
Orig.
Life
Evol.
Biosph.
41:621–632.
• Fournier
GP,
Gogarten
JP.
2007.
Signature
of
a
primi,ve
gene,c
code
in
ancient
protein
lineages.
J.
Mol.
Evol.
65:425–436.
• Fournier
GP,
Gogarten
JP.
2010.
Roo,ng
the
ribosomal
tree
of
life.
Mol.
Biol.
Evol.
27:1792–1801.
• Fournier
GP,
Huang
J,
Gogarten
JP.
2009.
Horizontal
gene
transfer
from
ex,nct
and
extant
lineages:
biological
innova,on
and
the
coral
of
life.
Philos.
Trans.
R.
Soc.
Lond.
B.
Biol.
Sci.
364:2229–2239.

55. References
(con,nued)
• Gal,er
N,
Tourasse
N,
Gouy
M.
1999.
A
nonhyperthermophilic
common
ancestor
to
extant
life
forms.
Science
283:220–221.
• Gogarten
JP,
Kibak
H,
Dierich
P,
et
al.
1989.
Evolu,on
of
the
vacuolar
H+-­‐ATPase:
implica,ons
for
the
origin
of
eukaryotes.
Proc
Natl
Acad
Sci
U
S
A
86:6661–6665.
• Gogarten
JP,
Taiz
L.
1992.
Evolu,on
of
proton
pumping
ATPases:
Roo,ng
the
tree
of
life.
Photosynth.
Res.
33:137–146.
• Gogarten-­‐Boekels
M,
Hilario
E,
Gogarten
JP.
1995.
The
effects
of
heavy
meteorite
bombardment
on
the
early
evolu,on-­‐-­‐the
emergence
of
the
three
domains
of
life.
Orig
Life
Evol
Biosph
25:251–264.
• Goldman
AD,
Bernhard
TM,
Dolzhenko
E,
Landweber
LF.
2013.
LUCApedia:
a
database
for
the
study
of
ancient
life.
Nucleic
Acids
Res.
41:D1079–82.
• Hao
B,
Gong
W,
Ferguson
TK,
James
CM,
Krzycki
JA,
Chan
MK.
2002.
A
new
UAG-­‐encoded
residue
in
the
structure
of
a
methanogen
methyltransferase.
Science
296:1462–1466.
• Harris
JK,
Kelley
ST,
Spiegelman
GB,
Pace
NR.
2003.
The
gene,c
core
of
the
universal
ancestor.
Genome
Res
13:407–412.
• Kim
KM,
Caetano-­‐Anollés
G.
2011.
The
proteomic
complexity
and
rise
of
the
primordial
ancestor
of
diversified
life.
BMC
Evol.
Biol.
11:140.
• Kingman
JFC.
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