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[Music]

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[Applause]

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good afternoon everyone this is a very

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aggressive AK with the other theories

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about ribosome evolution so I'm Jessica

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Bowman I work in Lauren Williams lab at

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Georgia Tech I'm part of the cool Center

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you might recognize this picture from a

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few minutes ago so what I'm going to

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talk to you today about is excavating

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the root of the tree of life this is a

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tree of life which is Jillian Banfield's

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so this is Gillian Banfield's new tree

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of life this is based on the 16

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different ribosomal protein sequences

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consensus of these you can see there's a

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lot of diversity here in bacteria we

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also have a lot of diversity or we're

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not quite as much in archaea and Eukarya

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and if we arbitrarily place Luca here so

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we're not rooting the Tree of Life we're

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just arbitrarily placing Luca here what

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we can do is look back and see if we can

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excavate this Tree of Life and ask the

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question whether the diversity of modern

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life what the diversity of modern life

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tells us about the evolution of biology

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before Luca so as many of you know this

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is the the ribosome we have a large

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subunit we have a small subunit the

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small subunit is responsible for

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decoding the large subunit contains the

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peptidyl transferase center which is the

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region of the ribosome in which the

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amino acyl Aidid trna transfers the

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amino acid to the growing polypeptide

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chain this is a ribosome structure by a

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hairy Nola's group we have the small

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subunit ribosomal RNA in blue the large

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subunit in gray there is a red tRNA here

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and the this is the piece art tRNA we

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know because there's an alpha helical

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structure of the growing polypeptide

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chain extending through this long exit

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tunnel and so the the useful thing for

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us is that we now have many different

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ribosome structures so we have ribosomes

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from all three trees of life to all

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three major branches and then some

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either crystal structures or cryo-em

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structures in the case of some of the

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more advanced eukaryotes so if we look

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at the e coli structure of ribosomal RNA

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this is a piece from the large subunit

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near the peptidyl transferase center

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what we can see is that we have a an RNA

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backbone here indicated in red this is

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of E coli bacteria we've superimposed

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this with a halo our Keela marichuy

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represented in our cans so from another

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domain of life and superimposed this

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with a yeast

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from the Eukarya and then with Homo

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sapiens and mitochondrial ribosomal RNA

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the same region of the large subunit

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what we see is that over 3.8 to 4

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billion years this ribosome really has

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not changed which is kind of amazing we

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can found this the boundaries of this

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conservation this conserved core as we

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call it we can resolve these boundaries

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within the ribosome with ribosomes of E

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coli of private caucus furiosa's which

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is another archaea and also within yeast

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down here we have the small subunit

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shown on the left the large subunit on

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the right the blue represents the common

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core of the ribosomal RNA for the large

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subunit the red here represents the

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common core of the small subunit if you

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notice if you look down this slide you

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begin to see that the gray portion which

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is the non common core or the RNA that's

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specific to that species seems to be

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increasing in proportion to the total

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amount of RNA and you would be right in

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that if you look at homosapiens

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ribosomal RNA you can see here this is

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the secondary structure in gray is what

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we call the common core and green these

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are expansion segments so the pieces of

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RNA that protrude beyond that common

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core and in pink here is one expansion

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segment in particular that I'm going to

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highlight so this is what we call es7 if

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we look at these expansion segments

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relative to the diameter of the sphere

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this common core and then what we call

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the eukaryotic shell that so the

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expansions beyond that common core

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that's universal to all organisms we see

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that these expansion segments especially

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expansion segments 7 and 27 of the human

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ribosome extend quite a long ways if we

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follow this expansion segment 7 which

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actually begins as a helix 25 in the

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e.coli ribosome you notice if we go to

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yeast here this purple is this helix 25

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it's growing as we then move and

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fruit fly and then into Homo sapiens if

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we look at this in three dimensions and

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someone emphasized earlier the

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importance of looking at

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three-dimensional structures instead of

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just sequences or two dimensional

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structures we see helix 25 this is from

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the e.coli the bacteria we can

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superimpose that with the crystal

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structure data of the archaea or the

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halo are Kili keyless Marist more dream

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and what we see is that the there

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appears to be a common ancestor of

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archaea in bacteria possibly we can a

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superimpose the archaea with yeast and

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see that the the ancestor of the yeast

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ribosomal RNA seems to be best

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approximated by an arcane and we can

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continue on with fruit fly and up to

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human this is quite a substantial

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elaboration on this three-dimensional

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structure to have begun with a helix

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that is conserved in bacterial today so

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what can this comparison of modern

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organisms tell us about the ribosome

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before the last Universal common

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ancestor so if we look closely at each

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of these sites of expansion in each of

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these expansion segments we see that

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there is a unique geometric fingerprint

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and most of them which we call an

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insertion site if you notice these two

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believe this is archaea and e-coli

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superimposed and this would be the

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eukaryotic expansion so this is kind of

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like the tree the trunk of a tree and a

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branch growing out of the tree

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so this ribosomal RNA grows without

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perturbing the common core this is helix

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52 so this is a portion of the ribosomal

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RNA that is different from the one I

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just told you showed you and this is

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helix 38 which is an entirely different

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expansion segment so we can make two

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observations one is that the modern

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ribosome post lucre grew and is growing

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by accretion and that the modern the

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second observation is that the modern

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ribosome post luca left some

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recognizable molecular finger

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so if we then combine those two with

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assumptions that the common core also

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grew by accretion and in the common core

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also left and in the common core

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these growth events or fingerprints were

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also left and we can go in and look at

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the common core of the ribosome for

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these insertion events and actually see

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back beyond the emergence of the last

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Universal common ancestor this is a

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model and it gives us a testable model

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so this is the superimposed helix 24 so

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this is actually in what we call the

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common core the ancestral expansion and

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here is a branch of ribosomal RNA coming

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out so this would be some kind of

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progression and the Luca R before Luca

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and we also see this type of insertion

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site in tRNA amazingly so this figure up

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here is entirely attributable to Anton

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Petrov in the back as this most of this

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presentation but if we look back to this

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common core and this is the common core

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of the large subunit here we can

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actually find these insertion sites all

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through the ribosome through the large

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subunit and each of these color

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transitions demarcates in a different

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insertion event in the last Universal

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common ancestor and these can be

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integrated through a progression over

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time and to generate phases possible a

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model of phases of like large subunit

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growth in which we have this phase one

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and phase two a dark blue and light blue

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this would be the peptidyl transferase

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one thing that wanted to emphasize is

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the effect of this model on the exit

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tunnel and the I guess the progression

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or folding or the the learning that

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proteins had to go through to fold at

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some point during evolution so this is

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the ribosome tRNA here in blue we have a

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growing peptide moving through the exit

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tunnel if we look at just the phase one

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so what we think is the oldest part of

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the large subunit and which is shown

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here

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and we progress through time consistent

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with our accretion model we add face to

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ribosomal RNA this develops an exit pore

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which would be this just the beginnings

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of this exit tunnel we add phase 3 phase

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4 phase five and faves six what we see

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is that the the most significant impact

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of this the phases and evolution of this

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in this model had to do with the

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elaboration and extension of the exit

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tunnel so there's a another person on

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our group Nick Kovacs who looked at

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protein folding over the different

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phases of the ribosome and found that

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the proteins that we don't have any

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ribosomal proteins in phase one but or

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two but in phase three the the proteins

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in Phase three are really characterized

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by these random coils and so this is

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unstructured protein and this has been

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shown by another graduate student from

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our group Katherine linear and then

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phase four we start to have some of

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these beta hairpins and then in Phase

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five we have more complex folds with

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these beta hairpins and some alpha

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helixes and so what we think is that the

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evolution of protein folding is

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concerted with the evolution of the exit

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tunnel I actually need to credit Moran

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sprinkle pinter with some interesting

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insights into this so what we think is

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that when the ribosomal RNA was in the

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early phases so it had only an exit pore

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no exit tunnel that in Phase three would

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have emerged random coral head times and

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as this exit tunnel became longer and

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longer we were able to accommodate these

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more advanced proteins so the idea is

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that when the exit tunnel is too short

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we de the formation of beta structures

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so we there's more likely to be

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aggregation that sort of thing so my

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conclusions today or that ribosomes

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evolved by chrétien of and without

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perturbation of four billion year old

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common core and that the evolution of

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the tunnel and protein folding were

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likely coupled

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I'd like to thank my group at Georgia

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Tech especially Lauren Williams the cool

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Center and our sponsors NASA and NSF and

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here is Anton our very important person

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in this work and also Nick Kovacs is

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here and moran and also peter was here

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right here all right thank you very much

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[Applause]

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we have time for a couple of questions

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destructor Southland and human I think

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at the time of Drosophila we probably

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would have had the more complex protein

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structures so the exit tunnel would have

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been closer to what we have today the

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address your question

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I just want to mention what they change

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something beyond the ribosome let me

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just comment on that the ribosomes

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throughout the three domains have all

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these kinds of weirds in insertions and

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deletions we do not know the functional

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aspects of those additions and deletions

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great it was really interesting one of

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the peculiar aspects of The Tree of Life

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is that there's these really long empty

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branches right and so your model seems

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to just suggest and I'm not saying it's

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not accurate but seems to suggest that

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somehow the bacteria the bacterial

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ribosome sort of stayed constant right

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and could form the node upon which the

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rest of the long you know the for the

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eukaryotes in archaea which you know it

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could be but that does require a lot of

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stasis for that bacterial ribosome which

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isn't reflected in the rest of the

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phylogeny yes I I don't know if you

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noticed but even in our bacterial model

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there's there's kind of a common even

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even though the e.coli structure

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ribosomal RNA is is approximates what we

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think is the common core they're not

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exactly the same so I think the that you

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coli may be a good approximation of an

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ancestral ribosome but is not

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necessarily something that was fixed in

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time in which eukaryotic ribosomes grew

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upon yeah you can speak to her after the

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segment because we are already running