Transcript Comparative genomics and structural biology of the

Comparative genomics and
structural biology of the
molecular innovations of
eukaryotes
L Aravind, LM Iyer, EV Koonin
Presentation by Ruben Valas
LECA
• Eukaryotes are very different than archaea
and bacteria
• There are no extant organisms that are
pre-eukaryote like
• This review paper examines some of the
structures that are unique to eukaryotes
Mixing of archaea and bacteria
Lopez-Garcia and David Moreira, 2006
Eukaryotes are very unique
• Nucleus with linear chromosomes
• Regulated cell cycle
• Cytoskeleton system
• Spliceosomal Introns
• Distinct posttranslational regulation
(ubiquitin)
• Organelles such as mitochondria
All of this happened fast
• Since all eukaryotes have these traits they
must have evolved in a very short period
of time
• Cavalier-Smith says this is quantum
evolution triggered by the mitochondrial
symbiosis
Structure changed 3 ways
• Ancient domains gained new functions
• Ancient folds were tweaked to form new
superfamilies
• New folds emerged
• This is a review paper, so this data comes
from looking at the structures other
papers identified
Innovations
Modification of Preexisting Domains
Their conclusions
• They conclude most innovations are α-
helical or chelation-supported
• α-helical and metal-supported structures
depend less on hydrogen bonding
between distant residues
• These structures can change rapidly
α-helical and metal-chelationsupported domains
My Data
• I can’t directly compare what we have
because they aren’t only using SCOP FSFs
• There are 60 SCOP FSFs that are only in
eukaryotes and are in at least 58 of the 61
eukaryotes in Superfamily
• If I use Dollo parsimony there are 123 or
145 FSFs in LECA depending on the tree
FSFs in LECA
60
123
145
A class(Zinc Binding)
21
52(1)
58(1)
B class
12
20
23
A/B class
2
3
3
A+B class(Zinc Binding)
13
27(1)
35(1)
Multidomain
2
4
5
Membrane
1
3
3
Small Proteins (Zinc Binding)
9(7)
14(10)
17(10)
Total Zinc Binding
8
12
12
Its not all alpha
• Their data is based on novel functions in
eukaryotes, some new structures take on
old functions
• I find more beta and alpha+beta than
metal binding, how these evolve rapidly
still needs to be established
• If alpha proteins can evolve so fast why
aren’t these folds seen earlier?
Duplications
• Many novel structures come from families
of paralogs
• These duplications appear to have
happened before LECA
• The mitchondrial symbiosis would act like
a gene duplication for many genes
Duplications predating LECA