Evolution of life's operating system revealed in detail

Jun 30, 2014
In the new study, Williams and Research Scientist Anton Petrov compared three-dimensional structures of ribosomes from a variety of species of varying biological complexity, including humans, yeast, bacteria and archaea. The researchers found distinct fingerprints in the ribosomes where new structures were added to the ribosomal surface without altering the pre-existing ribosomal core from the last universal common ancestor. Credit: Loren Williams/Georgia Institute of Technology.

The evolution of the ribosome, a large molecular structure found in the cells of all species, has been revealed in unprecedented detail in a new study.

Around 4 billion years ago, the first molecules of life came together on the early Earth and formed precursors of modern proteins and RNA. Scientists studying the origin of life have been searching for clues about how these reactions happened. Some of those clues have been found in the ribosome.

The core of the ribosome is essentially the same in all living systems, while the outer regions expand and become complicated as species gain complexity. By digitally peeling back the layers of modern ribosomes in the new study, scientists were able to model the structures of primordial ribosomes.

"The history of the ribosome is tells us about the origin of life," said Loren Williams, a professor in the School of Chemistry and Biochemistry at the Georgia Institute of Technology. "We have worked out on a fine level of detail how the ribosome originated and evolved."

The study was sponsored by the NASA Astrobiology Institute and the Center for Ribosomal Origins and Evolution at Georgia Tech. The results were published June 30 in the journal Proceedings of the National Academy of Sciences.

In biology, the genetic information stored in DNA is transcribed into mRNA, which is then shipped out of the cell nucleus. Ribosomes, in all species use mRNA as a blueprint for building all the proteins and enzymes essential to life. The ribosome's job is called translation.

The common core of the ribosome is essentially the same in humans, yeast, bacteria and archaea – in all living systems. The Georgia Tech team has shown that as organisms evolve and become more complex, so do their ribosomes. Humans have the largest and most complex ribosomes. But the changes are on the surface – the heart of a human ribosome the same as in a bacterial ribosome.

"The translation system is the operating system of life," Williams said. "At its core the ribosome is the same everywhere. The ribosome is universal biology."

In the new study, Williams and Research Scientist Anton Petrov compared three-dimensional structures of ribosomes from a variety of species of varying biological complexity, including humans, yeast, bacteria and archaea. The researchers found distinct fingerprints in the ribosomes where new structures were added to the ribosomal surface without altering the pre-existing core.

Additions to the ribosome cause insertion fingerprints. Much like a botanist can carve back twigs and branches on a tree to learn about its growth and age, Petrov and Williams show how segments were continually added to the ribosome without changing the underlying structure. The research team extrapolated the process backwards in time to generate models of simple, primordial .

"We learned some of the rules of the ribosome, that evolution can change the ribosome as long as it does not mess with its core," Williams said. "Evolution can add things on, but it can't change what was already there."

Explore further: Biologists find 'missing link' in the production of protein factories in cells

More information: Anton S. Petrov, et al., "Evolution of the Ribosome at Atomic Resolution." June 2014, PNAS, www.pnas.org/cgi/doi/10.1073/pnas.1407205111

add to favorites email to friend print save as pdf

Related Stories

Detour leads to antibiotic resistance

Mar 28, 2014

Ludwig Maximilian University researchers have used cryo-electron microscopic imaging to characterize the structural alterations in the bacterial ribosome that are required for induction of resistance to the ...

Mimicking living cells: Synthesizing ribosomes

Jun 29, 2013

Synthetic biology researchers at Northwestern University, working with partners at Harvard Medical School, have for the first time synthesized ribosomes—cell structures responsible for generating all proteins and enzymes ...

Study reveals how ribosomes override their blockades

May 14, 2012

Ribosomes are "protein factories" in the cells of all living things. They produce proteins based on existing genetic codes stored on special nucleic acid molecules. These molecules, also called messenger RNA (mRNA) due to ...

Recommended for you

DNA may have had humble beginnings as nutrient carrier

6 hours ago

New research intriguingly suggests that DNA, the genetic information carrier for humans and other complex life, might have had a rather humbler origin. In some microbes, a study shows, DNA pulls double duty ...

Central biobank for drug research

6 hours ago

For the development of new drugs it is crucial to work with stem cells, as these allow scientists to study the effects of new active pharmaceutical ingredients. But it has always been difficult to derive ...

User comments : 26

Adjust slider to filter visible comments by rank

Display comments: newest first

shavera
4.2 / 5 (6) Jun 30, 2014
Humans have the largest and most complex ribosomes.


this... bothers me. The implication is that we are somehow uniquely complex organisms, or that there is a directed goal to evolution (becoming human). Even if this is factually true, it is reinforcing a common confusion regarding evolution.
Torbjorn_Larsson_OM
4.4 / 5 (8) Jun 30, 2014
@shavera: I think I see what you are saying, but it doesn't need to be bothersome.

The article didn't compare many organisms, so the resolution of their claim is low. E.g. there are likely many organisms that have the same or larger complexity. There is 1 chance in 7 that we have the most complex ribosome among hominids alone (humans 1 species, chimps 2 species, gorillas 2 species, orangutans 2 species).

That humans are exceptional in any specific trait is unlikely. We haven't the largest genomes or cells (unicellular amoeba has both, I think). But that we in some case would differ from the average isn't, because there are many traits and evolutionary history is complex (so an average isn't saying much).

h20dr
2.1 / 5 (12) Jun 30, 2014
That last paragraph, to me, speaks of intelligent design.
Protoplasmix
3.3 / 5 (3) Jun 30, 2014
That last paragraph, to me, speaks of intelligent design.

I'm no expert on it, but it seems to me that a round wheel will roll down the hill of nucleic acid translation, while a square wheel won't. If that's an oversimplification of the process, and should humans one day improve upon the function of the ribosome with a new design, then I think it becomes a "chicken or egg came first" question. The hardware platform for consciousness exactly is what?
TheKnowItAll
5 / 5 (1) Jun 30, 2014
This is nice work, it leaves me wanting more species compared.

@Shavera: How would a writer know if anyone reads his/her work other than by reading back the reactions that he/she purposely caused? ;)
Whydening Gyre
4.6 / 5 (9) Jun 30, 2014
We are not a "culmination" of the evolutionary process - we are what survived...
Get over the anthropomorphic mindset...
malapropism
4.1 / 5 (9) Jul 01, 2014
That last paragraph, to me, speaks of intelligent design.


No it doesn't. It speaks to the fact that if the core ribosomal structure is changed then that is probably immediately fatal and therefore no organisms exhibit such evolutionary changes. However, adding stuff on to an already-successful evolved structure like the ribosome to make it "do more" is a feasible strategy for evolutionary advancement.

This is a little like, say, the flagellar "motor" where a sequence of evolutionary "improvements" can be seen through time and species complexity but mess with the basal mechanism that generates the movement of the flagella and it all stops working. Similarly, eyes and probably a bunch of other phenotypical characteristics. And btw, both of those examples used to be cited as "proofs" of "intelligent design by irreducible complexity". (Possibly they still are so cited, I don't bother to keep up with fundamentalist nutjobs' arguments; regardless that idea is well disproved.)
someone11235813
4.6 / 5 (10) Jul 01, 2014
Too bad Darwin didn't get to know what level of confirmation of his grand idea would be possible in the future. Much like the way astronomers in the 19th century wondered how we could ever possibly be able to know anything about the stars seeing as all we have to go on is a feeble bit of light and what can that reveal.
Torbjorn_Larsson_OM
4.6 / 5 (10) Jul 01, 2014
@h20dr: Why are you trolling science sites with magic agency ideas? That is shameful!

Besides, we already know that evolution is the process resulting in functional entities, see e.g. the provided illustration of it re ribosomes.

There is a deeper illustration of evolution in the kept core. Last year people found that the core genetic RNA machinery is catalytic, even one electron catalytic as today only proteins are, when exposed to Hadean/Archean conditions. E.g. an anoxic Fe2+ solute ocean evolved the rRNA/tRNA/mRNA as catalysts that were later coopted by evolution for genetic machinery. (Today's mRNA isn't generally catalytic as would then be predicted, but _old RNA functional genes_ are. E.g. the mRNA knife that self-excises introns type II (IIRC) and looks to be another evolutionary co-option in stem Archaea, now used by them and us.)
Torbjorn_Larsson_OM
4.5 / 5 (8) Jul 01, 2014
[ctd] This in turns connect RNA as evolving by co-opting the catalytic properties of a hot anoxic Fe2+ solute ocean itself. [Keller et al has shown that glycolysis and pentose pathways, and hence likely gluconeogenesis across semipermeable membranes, evolved in these conditions. And the pyrimidine based metabolic cofactors likely evolved from the pentose pathway and ambient ammonia. RNA strands is a side effect of their metabolism.]

But now we are looking at traits that evolved before darwinian evolution, likely by some form of lamarckian process acting on the Earth's early geophysical systems. RNA strands can crystallize replicators, repeats units over time and space, out of non-ordered strands in hydrothermal vents acting as hot/cold cycling synthesizers, driven by the same free energy 2nd law forcing as all other crystallization that also repeats units over time and space.
Torbjorn_Larsson_OM
4.5 / 5 (8) Jul 01, 2014
[ctd] A catalytic replicator would couple heredity to the existing metabolism (say, Russell et al's CO2/CH4 uptake as root metabolism*) and hence darwinian coevolution could have started. Peptides, especially dipeptides, would enhance the catalytic ability of such a "dirty RNA world" (metabolism, then RNA), so their co-option and coevolution are evolutionary predictive as well.

[*I have commented elsewhere on phys.org how a 2C root metabolism could feasibly produce the gluconeogenesis 3C hydrocarbons by thermodynamic targeting polymerization and oxidation already demonstrated by Keller et al & Russell et al metabolisms. That bottleneck, today bridged by many alternative pathways, seems to be predictive as well provided these metabolisms.]

Precisely as almost-life geophysical metabolic cells seem unavoidable given the Hadean environment, itself unavoidable given Earth's aggregation, live metabolic cells seem unavoidable. 2nd law organization couples to heredity under evolution.
Torbjorn_Larsson_OM
4.5 / 5 (8) Jul 01, 2014
But when I say "unavoidable", witnessed by the short period before we see life in the Archean, it is as all evolution contingent and constrained by the changing environment.

E.g. Mars may have remnant life in its crust, Europa may have life in its ocean, but it won't use exactly the same RNA bases at a guess. Sample return, now! If we pin down a handful of pathways that could have resulted in the observed evolutionary tree, same as we always test evolutionary trees up to some degree of unavoidable remnant loss of resolution, we will eventually need exoplanetary samples to increase resolution. E.g the pathways not taken.
Protoplasmix
5 / 5 (3) Jul 01, 2014
2nd law organization couples to heredity under evolution.

Interesting—is that a reference to the 2nd law of thermodynamics? Or is it referring to Mendel's laws? A google search only provided links to Mendel, genetics and inheritance, and even Moore's law showed up with respect to the digital coding of DNA. I'd be grateful if you could provide links to anything that I could study about it.
Torbjorn_Larsson_OM
4.4 / 5 (7) Jul 03, 2014
@Protoplasmix: I was unclear (short comment space), it is a reference to the 2nd law of thermodynamics (2LOT).

There is an old line of research attempting to couple 2LOT to life. The RNA strand paper uses it, but only superficially. You may instead want to look at England's papers that picks RNA as the unique (as far as we now know) self-replicator: "England, J. L. "Statistical Physics of self-replication." J. Chem. Phys., 139, 121923 (2013)." Link here: http://www.englan...ons.html

But the best use is Russel et al in the submarine alkaline hydrothermal emergence of life (in other hands, the "battery model" see e.g. NASA's astrobiology pages). Their "Turnstiles and bifurcators: The disequilibrium converting engines that put metabolism on the road", Biochimica et Biophysica Acta, 2014, is a generic simple introduction to non-equilibrium thermodynamics. http://www.scienc...12010420 (open access).
supamark23
5 / 5 (4) Jul 03, 2014
That last paragraph, to me, speaks of intelligent design.


Then you're hearing voices...
antigoracle
1.6 / 5 (7) Jul 03, 2014
Another "genius" response above, from the supamark23. One can only hope it's an evolutionary dead end.
Protoplasmix
4.2 / 5 (5) Jul 04, 2014
@Torbjorn -- awesome, thanks very much for those, that'll keep me busy for a while :)
verkle
1 / 5 (7) Jul 05, 2014
Somehow "Evolution" has been revealed in detail? Evolution is a dead end. There are so many unscientific bases in this theory that are getting nowhere. It is best to toss it out and stop wasting precious resources on it.

TheGhostofOtto1923
4.5 / 5 (8) Jul 05, 2014
Somehow "Evolution" has been revealed in detail? Evolution is a dead end. There are so many unscientific bases in this theory that are getting nowhere. It is best to toss it out and stop wasting precious resources on it.
Well I could say similar things about your religion except that there is overwhelming evidence which says that your religion is false, while there is overwhelming evidence which says that evolution is true.

So which should we toss out first? Hint - it is not the one that makes you feel good.
Torbjorn_Larsson_OM
5 / 5 (8) Jul 05, 2014
Don't mind the creo-tures.

They have science envy, because biology and especially evolution is so useful, while religiosity is only supported by dysfunctional (insecure) societies like Burma and US.

I'm reminded of Tom White, that responded to a creo-ture in one of his evolution (!) lectures. It's a highly worthwhile youtube clip, most amusing re crackpot tomfoolery. White pointed out that the building blocks of cells are today nucleotides (encode everything) and that is why we understand cancer evolution so well, how it evolves to eventually overwhelm the immune system and later evolve immunity to chemical treatments et cetera.

[And when he turns the smooth casts series of our ancestor skulls to show how we have nothing but incontrovertible evidence to shared ancestry, you get science shivers.]

Do creo-tures avoid cancer treatments or vaccines? I think not, but according to their own standards they should - because they claim they don't work and should be tossed out.
Torbjorn_Larsson_OM
5 / 5 (6) Jul 05, 2014
Come to think of it, even better, will creo-tures (as opposed to all the rest of us creatures, by ancestry), avoid gene sequencing to understand and perhaps treat genetic diseases, or investigate their own ancestry? Again, I think not, but it will become even more ludicrous to accept evolution but 'not' accept it.

Latest now, the Tibetan alleles that promote height tolerance without increasing hearth diseases (not using the increased blood cell count response but more efficient hemoglobin) was seen to a) have too little time to evolve by today's Tibetans and b) be of Denisovan ancestry. E.g. it is our bushy ancestry that provided the alleles, Denisovans were in Asia way before modern man was, and such an ancestry can't be squared with the magic agency myth texts.
Returners
1 / 5 (4) Jul 06, 2014
That last paragraph, to me, speaks of intelligent design.


No it doesn't. It speaks to the fact that if the core ribosomal structure is changed then that is probably immediately fatal and therefore no organisms exhibit such evolutionary changes. However, adding stuff on to an already-successful evolved structure like the ribosome to make it "do more" is a feasible strategy for evolutionary advancement.


No, silly, when you have a machine language, i.e. DNA and RNA, it runs in a specific way on a specific machine.

The reason you can't change the Ribosome's core is because it's a bit like a CPU on a computer. It takes specific chunks of data in a specific size and format and performs a specific set of instructions on that data. If you re-design the core, the code from existing "programs" becomes meaningless.

Did you also consider that interactions for some mechanisms may only have one possible configuration that actually works?

Returners
1 / 5 (4) Jul 06, 2014
The human Ribosome is protected against Broad Spectrum Antibiotics, which attack bacteria Ribosomes, which is why most bacteria cannot adapt to broad spectrum antibiotics, while human patients are safe from the effects. The problem is the ones that do tend to be very, very bad.

At any rate, if you changed the mechanism of the Ribosome the coding for the mRNA would no longer produce the same chemistry when they come in contact, and therefore would not necessarily produce the same proteins.

Simple organisms don't need complex tools, so there is not necessarily a reason for a creator to give them complex tools.

Complex organisms need more complex tools: controlling when cells differentiate, activating related genes, and so forth, and that explains why a multi-celled organism would have a more advanced Ribosome, just as your PC or smartphone has a more advanced processor core than does a digital watch.

The evidence supports design much more than evolution. Always has.
Uncle Ira
4 / 5 (4) Jul 06, 2014
The evidence supports design much more than evolution. Always has.


So far the evidence supports a design flaw in your mind Returnering-Skippy. If I were you I'd be asking the designer for a refund.
TheGhostofOtto1923
3.7 / 5 (3) Jul 07, 2014
The EVIDENCE supports design much more than evolution. Always has
Lrrkrrr. Cosmologist, climatologist, software engineer, physicist... Polymath. Where in the ribosome does it say that graven images are an abomination? Where does it tell us we have a soul? Where in our DNA can we find the edict to observe the sabbath or expect to be killed?

Science may one day find evidence of a creator god in our genes (they won't.) But guaranteed it will not be the god who wrote a book full of things which never happened and people who never existed.

You really should try to focus on the overwhelming EVIDENCE that your god is a lie.
Whydening Gyre
not rated yet Jul 07, 2014
Simple organisms don't need complex tools, so there is not necessarily a reason for a creator to give them complex tools.

Complex organisms need more complex tools: controlling when cells differentiate, activating related genes, and so forth, and that explains why a multi-celled organism would have a more advanced Ribosome, just as your PC or smartphone has a more advanced processor core than does a digital watch.

The evidence supports design much more than evolution. Always has.

Returners...
The Universe IS the designer. Using one simple equation, a+b+c, (ie - 1+1= the new 1)everything in it is provided for us to ponder and go "Holy Crap! Didn't see THAT one coming..."