Download #315: Ribosomes: Unlocking the secrets to your cellular protein

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#315: Ribosomes: Unlocking the
secrets to your cellular protein
factories
VOICEOVER
This is Up Close, the research talk show from the University of Melbourne, Australia.
DYANI LEWIS
Hi I'm Dyani Lewis. Thanks for joining us. If I were to say the word, protein, you'd
probably think of a juicy steak or perhaps a muscle-building protein shake. But in our
bodies proteins give us far more than just muscular bulk. They're the enzymes that
carry out cellular reactions, the microscopic sensors that allow us to detect the smell
of a rose or the pain of a burn. They're the cement that connects our cells together;
give our nose cartilage its rigidity and our skin its elasticity and they serve all of these
incredible functions in organisms from the lowly bacterium to the majestic Sequoia
and everything in between.
But proteins in their myriad forms could not exist without a complex piece of cellular
machinery known as the ribosome. As important as it is, the ribosome, unlike the
proteins it makes, is hardly a household name. But today on Up Close we get an
intimate tour of the ribosome, led by perhaps one of the best qualified people to
speak about it. Professor Ada Yonath won the Nobel Prize in Chemistry in 2009 for
her pioneering work on the structure of the ribosome. She's now the Director of the
Helen and Milton A Kimmelman Centre for Biomolecular Structure and Assembly at
the Weizmann Institute of Science in Israel. Welcome to Up Close, Ada.
ADA YONATH
Thanks for inviting me.
DYANI LEWIS
Ada the ribosome was discovered only quite recently in the 1950s I believe, did we
know at that time that it had such an important role in protein synthesis?
ADA YONATH
Yeah I think so because it was before the ribosome was discovered. Once the DNA
structure and the sequence of the information in it were revealed, were discovered,
and once the genetic code and its relation to the protein structure, which is dictated
by the sequence of the protein component, once all this was found, the question was
where is it done and how is it done? So for ribosomes unlike many other cellular
components there was a search. Scientists wondered where is it done and how is it
done and what are the sub-processes or sub-components.
My understanding is that they found that there is a region in every cell that makes
proteins. It's a cellular component or cellular location. And at that time it was
traditional to think this way because they knew very little about the cell. Everybody
knows there are no clues and here is the DNA. So it's a cell component. Now we
know that even nuclei have structure, have component, can be described in detail.
So I think that they thought about the fraction of the cell that understands the genetic
instructions because actually the genetic code is just a list of instructions. These
instructions are being transferred to proteins in a place on the cell, like every cell has
a membrane, so maybe every cell is a compartment, it makes proteins.
So they looked for it. Then it was on the specific component of the cell called RNA is
a deeply involved in it, it was not clear how and the general idea was that proteins
are making themselves because they can make, as you said earlier, almost
everything. But there is a component RNA nucleic acid, it's like DNA, it's very
similar. So people looked for these regions that RNA reach. I think this is the way it
started. Until a scientist, Palade, that when he found it out he was already American
but actually a refuge from Romania. He showed that in this part of the cell, in this
compartment there are bodies, there are components, assemblies something like
this. He didn't know exactly what.
And he showed that if he takes them, if isolates this fraction from the cell and use all
the ingredients it gets proteins. So this is the first time people understood that it's not
just a component, it's bodies within the component like multi-component aggregate.
These bodies were called Palade bodies and then they still were considered to be
aggregate of many things, with no internal order and with no list of functions, one
after the other that has to be done. Only when another very important person,
Nomura, a Japanese that lived in the States, showed that these bodies are made of
components that have fixed relations between them, one to one all of them. Only
then scientists started to think about cellular factories. So the ribosomes were the
universal cellular factories because every ribosome can get every instruction and
make a protein correctly out of it. Ribosome of bacteria can get instructions from a
rat, from a tree, from an elephant even from the dinosaurs and can make the
requested protein.
DYANI LEWIS
You mentioned RNA, ribonucleic acid and it is very similar to DNA. Is this a major
component of the ribosome?
ADA YONATH
Yeah, all ribosomes work the same way and after the structures were determined,
part of it is my work, it was shown that in the ribosome RNA is doing all the tasks, not
like what you said earlier and I didn't oppose, that proteins are doing almost
everything. Proteins are not making themselves. For this I think that nature is
clever. It has two kingdoms and one kingdom makes the other. Otherwise maybe
there would be some type of bias. But in all ribosomes RNA is the machine and in all
ribosomes except for mitochondria, that's the ribosomes that make energy, except
for them, RNA is at least two-thirds of the structure, of the mass of the structure. In
mitochondria it's half-half. So there are many, many proteins, ribosomal proteins, in
humans 80, in bacteria 55. It's many. But the RNA does the job.
DYANI LEWIS
The RNA, it's usually thought of as a molecule that carries genetic information. You
mentioned before it carries information from the DNA in the nucleus of the cell to the
ribosomes. How is it that it can do these extra activities in the ribosome?
ADA YONATH
So RNAs not only carry off information. In the beginning they thought it's a carrier of
information. It is a carrier of amino acids these are the components that make the
proteins. It's called transfer RNA. The RNA that comes through as genetic
information is called messenger RNA and then there is ribosomal RNA. In the
beginning of ribosomes for at least three decades, people thought that RNAs does is
a skeletal that keeps the whole thing together. They didn't expect it to have
enzymatic properties, chemical properties. But then some other RNA machinery,
small ones were discovered, maybe 15 or 20 of them, not many. But they can do
chemistry, like RNA enzymes and called ribozymes. Also recently the last I think 15,
20 years, small RNA fragments were identified and they play a major role in
regulation, what will be translated, what not. It's called microRNA or small RNA.
There is also a transcript of part of a gene that don't call for proteins, called for these
small RNAs. Next year there is a Nobel Prize that was given to small RNAs a year
before us.
DYANI LEWIS
It's a very versatile molecule, certainly more versatile than its better known relative I
guess you could say DNA which is the main carrier of our genetic information in our
genome. Does this mean that RNA has a more important role in I guess the
evolution of life itself?
ADA YONATH
There are several hypotheses of how biology came into the world. There was a
world that was not biological. It had clay and metals, maybe it was happy, maybe it
was not happy like most of the stars today. Then at one point, I don't know if it's all
of a sudden or very, very slow, life began. One of the theories is that there was an
RNA world, before life RNA could exist in this very clay-metal environment and it
could do all what RNA wanted. It may say copy itself, extend itself, cut itself,
whatever it was needed for the primitive life of RNA.
In recent decades there are voices that say RNA couldn't be alone, must be
something else, for instance at least amino acids that were shown that they came
into our planet from lightening.
DYANI LEWIS
These are the building blocks of proteins?
ADA YONATH
Yeah, yeah. So these building blocks are very clever. They snatched the machines
that connect parts of RNA together and snatch it for connecting themselves. So in
this way, I continue the hypothesis, in this way small, little proteins completely
accidental were produced and those that were needed in the RNA world survived,
not because they were more pretty or were longer or shorter, they were needed.
Then life was built around this little RNA machine that made them and we think that
we detected this little prebiotic machine in every ribosome that functions today. So
we are very excited about it.
DYANI LEWIS
This collaboration between the RNA and all of the functions that it can do and then
the amino acids come in, it's really given us life as we know it today then?
ADA YONATH
Yeah. So life today is made of RNA, DNA, proteins and fatty acids or some type of
this. Fatty acid could be made by RNA with no problem and proteins have some
problem, but they just snatched one of the existing RNA machineries. We collect this
machinery, the Proto-Ribosome. Proto because we think that maybe there was even
a 'pre-Proto-Ribosome'. This is what RNA enjoyed for itself.
DYANI LEWIS
This is Up Close. I'm Dyani Lewis and in this episode we're talking about ribosomes
with Nobel Prizewinning crystallographer Ada Yonath.
Ada you used a technique called X-ray crystallography to work out the structure of a
ribosome. How does X-ray crystallography actually allow you to determine what a
molecule looks like?
That's a really good question for today because this is the Year of Crystallography,
2014 was announced to be the Year of Crystallography. Not by me, by UNESCO
and UN, it means it's all over the world. And the reason that it's this year; it's the
year that the Nobel Prize was given to Max von Laue who showed how x-ray are
diffracted from materials. This is the clue. X-rays or Roentgen rays are the only rays
that can function at wavelength which can show distances between atoms, it means
how molecules are made. But there are no lenses for x-rays. X-rays are very useful
in medicine and in many other applications but also in diffraction because they don't
have the wavelength. You can decide which wavelength you want and tune it to that
and this is non-technique, and then materials are diffracting them, every material.
The question is if we can measure this diffraction because we are just human beings
and materials are much more clever than we are. So the only way so far that we can
measure - since the diffraction is continuous, we don't know how to measure
continuous so we need discrete points. The only way to get discrete points is to
pack the material that we want or the compound that we want to investigate in
crystals. So the periodicity of the crystal or the reverse of it doesn't matter, and
some may function of the periodicity of the crystals together with the diffraction end
up in spots.
DYANI LEWIS
Sorry, because all of the molecules are lined up?
ADA YONATH
Yeah, periodically and they contribute will to the same direction. Since this branch of
science was established and became useful which is just a hundred years ago,
actually it became useful only eighty years ago, and for biological molecules only
sixty years ago; 38 out of 110 years of Nobel Prize, 38 were given to investigations
that are either directly by crystallography or the data or the discoveries that were
made were based on crystallography.
DYANI LEWIS
That's incredible.
ADA YONATH
So I think that it's incredible and thank you for giving me the chance to say it.
DYANI LEWIS
Now your interest obviously the ribosome is in every living organism, so how did you
decide which ribosome to use to look at the structure?
ADA YONATH
Well I think the ribosome decided on me because as we already discussed crystals
are needed and ribosomes are modular components and very dynamic and not long
lasting. Obtaining a crystal of them was - I don't want to see was not easy, I want to
say was not possible - and it was considered to be formidable for crystallisation. So
my greatest thing is to identify which ribosomes had the chance to crystallise and I
did, it worked.
DYANI LEWIS
So you tried a few different ribosomes from different organisms did you?
ADA YONATH
No so many. One or two organisms that were popular between the ribosomologists
before my time, I read what they tried to do with them so I didn't have to try and fail
again. It was enough that somebody else failed. I even talked to some of them. I
understood that it should be difficult or impossible to crystallise ribosomes if we don't
do something. So I sort of gave up, not gave up I didn't even start. I wanted to
understand protein biosynthesis but there are factors that tell the ribosomes start and
that tell ribosomes stop and all type of factors and I thought that they are more
doable. But anyway I tried to experiment but in between I had an accident and while
recovering I read. I read all types of things that I wouldn't have read otherwise
because all of a sudden I had time and I could expand myself.
I read about a delegation that went to the North Pole looking at the metabolism of the
sleeping bears. They were interested in metabolism as a whole but they looked at
everything. They saw that on the internal side of the membranes of every cell in the
bears, the ribosomes are periodically packed what people couldn't achieve and the
bears could, or maybe nature produced this mechanism. They looked it as a side
finding. If me or two more scientists wouldn't read it, it would be just buried. But I
read it and then I thought, ah, under stress or when the cell feel that stress is going
to come they pack the ribosomes in an organised way. Ribosomes do not exist more
than four or five days and the winter is very long, so when the bears get up from their
sleep and they want to do all types of things that bears are doing they need proteins
and then they need ribosomes. If ribosomes are not protected they will deteriorate.
So I thought stress is what I should exploit in order to get crystals.
So actually I worked only on three different bacteria, all of them crystallised.
Knowledge about how these bacteria live was a good start. I thought that if bacteria
lives at 80 degrees centigrade or in the Dead Sea where there is no other life, they
must have robust ribosomes. So a little bit of shock to this on both ribosomes did it.
DYANI LEWIS
Now biomolecules especially very large ones like the ribosome you were mentioning
there composed of the RNA as well as 50 or 80 proteins; they're not very rigid
structures. When a molecule gets that large they flex and move around. How does
crystallography account for this when you need very periodic crystals?
ADA YONATH
Okay. So first of all they not only flex and move around, they have inherent mobility
and flexibility that allows them to do their function. It's inherent in them. It's not just
that they're allowed. Maybe they are large in order to do what they do. So
crystallography needs a stationary state. Crystals have to be crystals. They have to
be periodic in all the dimensions, three dimensions and very well packed. We are
trying to be as close as possible to the functional state. The crystallisation of course
is done under conditions that are not completely normal but we are trying not to
deviate a lot. Second, in all crystals of biological materials including ribosomes, the
connection between one molecule, one compound to the second, is minute.
They are covered by the solution. For instance in ribosomes one of the better crystal
forms is 80 per cent solution. It's even less packed like in the cell and in water. But
in order to be sure that what we see is functionally relevant we are trying to cocrystallise the molecule, in this case ribosomes with the substrate or with their
inhibitors or with whatever binds to them with their factors. And if we can crystallise
them with their substrate and see the substrate in the crystal form, we have much
higher trust in it. In many cases we can do the experiment in the crystal. We can put
the substrates and we can get the product in the crystal then we are celebrating.
Then we are really sure.
Because ribosomes they have many functional states so in order to understand it, I
found a way to merge together structures that were trapped in different functional
state and if we put all of them, one next to the other, I could see how they go from
one to the other. In this way we have the dynamics, maybe not all the dynamics, not
every but a lot. We got it and we understand flexibility and best, we understand their
function.
DYANI LEWIS
So you've got a sequence of snapshots of ribosomes doing various stages of the
process.
ADA YONATH
Well each snapshot is about a million observations. If we find a way to merge them
and to interpolate between them, [it's like there the] interpolation is the trick.
DYANI LEWIS
I'm Dyani Lewis and my guest today is Chemist, Ada Yonath. We're talking about
her Nobel Prizewinning work on the ribosome, here on Up Close.
Ada, once we have worked out the structure of the ribosome, what more is there to
do? I mean once we have that series of snapshots, you've continued to work on the
structure of the ribosome, why is that?
ADA YONATH
Yeah, I could go to Fiji Islands and start endless vacation. But we don't understand
everything yet. There are lots and lots of open questions. We still don't know much
about human ribosomes and here the interest is also in diseases, for instance in
cancer where cells grow indefinitely and fast. Ribosome has to work indefinitely and
fast. What happens? More ribosomes or each ribosome is more efficient? That's a
very important question if we think about combat something like cancer. So this is
one.
Second is antibiotics that are used for where bacteria that make diseases, bacteria
that are pathogenic. Half of the antibiotics that are useful clinically are targeting
ribosomes because ribosomes are like factory. I called it early factory but they really
work like this, in assembly line in a factory. It's enough to just stop one, one step of
the line and that's it. The product will not come out. So that's like in the ribosome.
There are several functional sides and antibiotics paralyse them, hamper them.
Antibiotics, the situation with them is very dangerous right now because resistance is
showing up in very fast pace, so we are now trying to not only understand how the
antibiotics bind but we look for ways to minimise resistance, maybe not combat it
completely but minimise. So that's another thing that is interesting.
DYANI LEWIS
So that's through understanding the exact structure of the binding. How does that
help to overcome resistance?
ADA YONATH
I can't tell you yet but we have ideas. In general if one knows how antibiotic binds
and we know what was changed in the ribosome of the bacteria in order to minimise
or even stop the binding, we see what was changed and we can try to make the
antibiotic with components that will bypass the change. The change is the genetic
mutation of the bacteria. Bacteria, their lifetime until they have children is between
10 minutes to six hours. So their slowest is six hours, four generations a day. We
need a hundred years for four generations and those that are living two, three hours
even six generations a day. So they can have forward mutating themselves endless
and the one that survives, it means that it doesn't bind the antibiotic. It survives and
it stays. We cannot stop their ability to mutate themselves, but we can try to make
the antibiotic such that simple mutation will not avoid binding.
DYANI LEWIS
So how does crystallography complement other techniques like mutational studies
where you can mutate different parts of the ribosome or proteins for instance? How
does that technique work with crystallography?
ADA YONATH
Okay. So bacteria don't know crystallography so they mutate themselves as I said
earlier, they mutate endlessly until one wins. This is more or less the way that
mutations in agriculture led to much better food or amount or taste or whatever by
mutations that we didn't even understand. This is the story of agriculture for
instance. It's easy to explain. In our studies, in modern studies we look what was
changed. We look at the structure. We determine the new structure. We see what
was changed and we try to put a piece of wood into it - piece of something - that will
avoid this possibility to change. Sometimes it requires a lot of structures and then
interpretations of the structures and then chemistry. But it's always less than blind
search.
DYANI LEWIS
And do you think that things like computation methods that try to solve complex
structures, do you think that they will ever supersede crystallography for determining
molecular structures?
ADA YONATH
I have very little hope about this. I know that 40 years ago there were some
scientists that said they will understand all their energetics was in a protein or was in
the molecule and they will compute it. So this was in the '60s. Last year the Nobel
Prize was given to three of these guys. But not because they could determine a
structure by computation, this is Warshel, Levitt and Karplus, but because they could
compute or understand or find the energetical terms of non-structures or of structure
next to another structure. But the input is from crystallography. They can compute
but they need an input. They need something to build on.
DYANI LEWIS
Crystallography will be around for a while longer.
ADA YONATH
I'm not sure because now people try to make crystallography without crystals but not
by computing.
DYANI LEWIS
Ada, thanks for being our guest today on Up Close.
ADA YONATH
Thank you for inviting me. It was a pleasure to talk to you.
DYANI LEWIS
Professor Ada Yonath is a Nobel Prizewinning chemist and Director of the Helen and
Milton A Kimmelman Centre for Biomolecular Structure and Assembly at the
Weizmann Institute of Science in Israel. If you'd like more information or a transcript
of this episode, head to the Up Close website. Up Close is a production of the
University of Melbourne, Australia. Created by Eric van Bemmel and Kelvin Param.
This episode was recorded on 20 August 2014. Producers were Kelvin Param, Eric
van Bemmel and me, Dr Dyani Lewis. Audio engineering by Gavin Nebauer. Until
next time, goodbye.
VOICEOVER
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© The University of Melbourne, 2014. All Rights Reserved.
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