Scientists capture most detailed images yet of humans' tiny cellular machines

Jun 02, 2014 by Kelly April Tyrrell
U6 RNA is red and the four RRMs of Prp24 protein are beige, orange, aqua and purple, with linkers in gray. Credit: Brow and Butcher Labs

A grandfather clock is, on its surface, a simple yet elegant machine. Tall and stately, its job is to steadily tick away the time. But a look inside reveals a much more intricate dance of parts, from precisely-fitted gears to cable-embraced pulleys and bobbing levers.

Like exploring the inner workings of a clock, a team of University of Wisconsin-Madison researchers is digging into the inner workings of the tiny cellular machines called spliceosomes, which help make all of the proteins our bodies need to function. In a recent study published in the journal Nature Structural and Molecular Biology, UW-Madison's David Brow, Samuel Butcher and colleagues have captured images of this machine, revealing details never seen before.

In their study, they reveal parts of the spliceosome—built from RNA and —at a greater resolution than has ever been achieved, gaining valuable insight into how the complex works and also how old its parts may be.

By better understanding the normal processes that make our cells tick, this information could some day act as a blueprint for when things go wrong. Cells are the basic units of all the tissues in our bodies, from our hearts to our brains to our skin and lungs.

It may also help other scientists studying similar cellular machinery and, moreover, it provides a glimpse back in , showing a closer link between proteins and RNA, DNA's older cousin, than was once believed.

"It gives us a much better idea of how RNA and proteins interact than ever before," says Brow, a UW-Madison professor of biomolecular chemistry.

The spliceosome is composed of six complexes that work together to edit the raw messages that come from genes, cutting out (hence, splicing) unneeded parts of the message. Ultimately, these messages are translated into proteins, which do the work of cells. The team created crystals of a part of the spliceosome called U6, made of RNA and two proteins, including one called Prp24.

Crystals are packed forms of a structure that allow scientists to capture three-dimensional images of the atoms and molecules within it. The crystals were so complete, and the resolution of the images so high, the scientists were able to see crucial details that otherwise would have been missed.

The team found that in U6, the Prp24 protein and RNA—like two partners holding hands—are intimately linked together in a type of molecular symbiosis. The structure yields clues about the relationship and the relative ages of RNA and proteins, once thought to be much wider apart on an evolutionary time scale.

"What's so cool is the degree of co-evolution of RNA and protein," Brow says. "It's obvious RNA and protein had to be pretty close friends already to evolve like this."

The images revealed that a part of Prp24 dives through a small loop in the U6 RNA, a finding that represents a major milestone on Brow and Butcher's quest to determine how U6's protein and RNA work together. It also confirms other findings Brow has made over the last two decades.

"No one has ever seen that before and the only way it can happen is for the RNA to open up, allow the protein to pass through, and then close again," says Butcher, a UW-Madison professor of biochemistry.

Ultimately, Butcher says they want to understand what the entire spliceosome looks like, how the machines get built in cells and how they work.

While this is the first protein-RNA link like this seen, Brow doesn't believe it is unique. Once more complete, high-resolution images are captured of other RNA-protein machines and their components, he thinks these connections will appear more commonly.

He hopes the findings mark a transition in the journey to understand these cellular workhorses.

"It's exciting studying these machines," he says. "There are only three big RNA machines. Ours evolved 2 billion years ago. But once it's figured out, it's done."

The U6 crystal structure was imaged using the U.S. Department of Energy Office of Science's Advanced Photon Source at Argonne National Laboratory. The work was funded by a joint grant from the National Institutes of Health shared by Brow and Butcher.

Explore further: RNA controls splicing during gene expression, further evidence of 'RNA world' origin in modern life

More information: Animation, study paper: www.nature.com/nsmb/journal/va… b/nsmb.2832_SV1.html

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JVK
1 / 5 (2) Jun 02, 2014
Re: "No one has ever seen that before and the only way it can happen is for the RNA to open up, allow the protein to pass through, and then close again," says Butcher, a UW-Madison professor of biochemistry.

That was predicted in the context of cell type differentiation in our model, which linked the conserved molecular mechanisms of alternative splicings of pre-mRNA to nutrient-dependent cell type differentiation in individuals of species from microbes to man.
http://www.hawaii...ion.html

Jon Lieff has since provided the most detailed representation of predictable cause and effect that I have seen.
http://jonlieffmd...volution

Evolution is actually nutrient-dependent pheromone-controlled ecological adaptation. The reason theorists didn't realize that fact is that they were taught to believe that mutations and natural selection led to biodiversity. Silly theorists!
anonymous_9001
5 / 5 (2) Jun 03, 2014
That was predicted ... in our model


What? No it wasn't. Your 1996 paper talks about the potential role of splicing, not how the spliceosome works or its structure.
Writela
not rated yet Jun 03, 2014
Most detailed picture / 3D animation of neural synapse
JVK
1 / 5 (2) Jun 03, 2014
We linked nutrient-dependent cell type differentiation via alternative splicings of pre-mRNA to sex differences in the cell types of yeasts and other differences in cell types that are controlled by the physiology of reproduction, which is pheromone-dependent. The model was extended in 2000 to insects and in 2005 to their life history transitions, which will lead others -- like you -- to complain about the model as they try to redefine "mutation" and force their definitions to fit what they cannot fit. They cannot fit into a model of ecological variation that results in ecological adaptations because mutations are not involved in adaptations. Pre-existing genetic variation is!

"The study also shows that stickleback evolution is accelerated by the use of pre-existing genetic variation, instead of waiting for new, random mutations to arise, Wray explains."
http://www.nature...20120410
anonymous_9001
5 / 5 (1) Jun 03, 2014
If your assignment were to not read what I wrote and make an incredibly irrelevant response, I'd give you an A+.

You quoted an excerpt about the molecular structure of the enzyme that they elucidated. You then said "that's what we predicted!", which is beyond false. You never studied the structure of the spliceosome, so why on Earth would you say that? It was probably one of your most irrelevant and off topic comments to date.
JVK
1 / 5 (2) Jun 03, 2014
One need only understand a little bit about physics, chemistry, and how they contribute to the conserved molecular mechanisms of alternative splicings in species from microbes to man to predict that nutrient-dependent pheromone-controlled ecological adaptations will be found in species from microbes to man. Details of seemingly futile cycles of protein biosynthesis and degradation can then be considered in the context of themodynamics and organism-level thermoregulation, which is why I have since also addressed those aspects of ecological adaptations.

Ecological adaptation is what we predicted, and that's what has been found, which makes our 1996 Hormones and Behavior review article relevant to everything else that's been published since then about alternative splicings that link the epigenetic landscape to the physical landscape of DNA in organisms from microbes to man.

Please tell us how mutations and natural selection lead to evolution and biodiversity for comparison.
Captain Stumpy
5 / 5 (1) Jun 04, 2014
Evolution is actually nutrient-dependent pheromone-controlled ecological adaptation. The reason theorists didn't realize that fact is that they were taught to believe that mutations and natural selection led to biodiversity. Silly theorists!
@jk
your model creates mutations, which then actually enhance as well as support the theory of evolution as well as undermine your idiotic attempt to denigrate mutations and the people who prove it works (like Lenski) like the theorists said... silly kohl![qOne need only understand a little bit about physics, chemistry lets see... coming from a self professed college failure, this is not very impressive, especially when you cannot even get your own model right in your head.

I would listen to anonymous_9001. He speaks fact and the more you talk, the worse you look
nutrient-dependent pheromone-controlled ecological adaptations
AKA MUTATIONS
Captain Stumpy
5 / 5 (1) Jun 04, 2014
Please tell us how mutations and natural selection lead to evolution and biodiversity for comparison.
@jk
well... lets see
since you said that your model creates mutations, then your own model is a good example of how mutations and natural selection lead to evolution. Especially in light of our conversation where I asked
DOES your model make any changes to the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element?
This is a yes or no answer
(this is the DEFINITION of Mutation) to which you answered
YES!
--Thanks for asking
so we KNOW that your model creates mutations
This is not disputable as you've already admitted it

so any other questions?
I am sure Lensji could set you straight on a few other issues too http://myxo.css.m...dex.html

and I would love to see you explain how you think he refuted mutations...
anonymous_9001
5 / 5 (1) Jun 04, 2014
Ecological adaptation is what we predicted, and that's what has been found, which makes our 1996 Hormones and Behavior review article relevant to everything else that's been published since then about alternative splicings that link the epigenetic landscape to the physical landscape of DNA in organisms from microbes to man.


Are you saying alternative splicing is responsible for genetic diversity?
JVK
1 / 5 (1) Jun 04, 2014
Are you saying alternative splicing is responsible for genetic diversity?


I wrote: "One need only understand a little bit about physics, chemistry, and how they contribute to the conserved molecular mechanisms of alternative splicings in species from microbes to man to predict that nutrient-dependent pheromone-controlled ecological adaptations will be found in species from microbes to man. Details of seemingly futile cycles of protein biosynthesis and degradation can then be considered in the context of themodynamics and organism-level thermoregulation, which is why I have since also addressed those aspects of ecological adaptations."

What do you think I'm saying?
What do you think Jon Lieff is saying in Alternative RNA Splicing in Evolution? http://jonlieffmd...volution

"In fact, recent research shows that alternative splicing may be the critical source of evolutionary changes differentiating primates and humans...."
JVK
1 / 5 (1) Jun 04, 2014
I am sure Lensji could set you straight on a few other issues too


Do you think Jon Lieff should set Lenski straight? http://jonlieffmd...volution

"In fact, recent research shows that alternative splicing may be the critical source of evolutionary changes differentiating primates and humans...."

If alternative splicing is the critical source of nutrient-dependent pheromone-controlled ecological adaptations, someone needs to set all of the pseudoscientists straight, which is what Dobzhansky (1964) said 50 years ago when he called them bird-watchers and butterfly collectors.
anonymous_9001
5 / 5 (1) Jun 04, 2014
It's a yes or no question.

Are you saying alternative splicing is responsible for genetic diversity?

Lieff is not at odds with Lenski. Regulatory networks and gene sequence work together to make the phenotype.

JVK
1 / 5 (1) Jun 04, 2014
I'm saying that biodiversity is nutrient-dependent and pheromone-controlled via conserved molecular mechanisms in species from microbes to man. The reason I am saying that in those words is so that anonymous fools and idiot minions of biology teachers like PZ Myers cannot twist what I'm saying (like SSGT Stumpy has done).

Overall, however, if you cannot understand what I have been saying in a series of published works for more than 17 years, you should quit asking what I'm saying and tell me what you have published or clearly detailed about whatever pseudoscientific nonsense you think explains the biodiversity on this planet.

Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
http://figshare.c...s/994281
anonymous_9001
5 / 5 (1) Jun 04, 2014
Yes or no answer. It's very simple. You can't twist a yes or no answer.

Based on this quote from you:

Ecological adaptation is what we predicted, and that's what has been found, which makes our 1996 Hormones and Behavior review article relevant to everything else that's been published since then about alternative splicings that link the epigenetic landscape to the physical landscape of DNA in organisms from microbes to man.


is splicing responsible for all the genetic variation and diversity?
Captain Stumpy
not rated yet Jun 04, 2014
The reason I am saying that in those words is so that ... cannot twist what I'm saying (like SSGT Stumpy has done)
@jk
no one twisted your words but you
THAT was one of my points. it remains one of my points
I just let you/others know- If YOU cannot comprehend the lexicon if your chosen field of study
then coming here to rant and vent your fallacious claims and pseudoscience only proves that YOU are the "idiot minion" and "pseudoscience hack"

After all, YOUR MODEL is but a small part of the known mechanisms of evolution

why not just answer? you are SUPPOSED to be a scientists and published. JUST ANSWER
is splicing responsible for all the genetic variation and diversity?
this is a yes or no answer
the only reason you would NOT answer clearly and precisely is because YOU DONT KNOW or YOU DONT WANT TO LOOK STUPID because you KNOW that your going to get caught in another lie/misinterpretation/false assumption and proven wrong and have your words used against you
AGAIN
Captain Stumpy
not rated yet Jun 04, 2014
if you cannot understand what I have been saying in a series of published works for more than 17 years, you should quit asking what I'm saying and tell me what you have published
@jk
given that YOU YOURSELF cannot understand what you are publishing, it would be much more productive for YOU to clarify your statements here than to continually post the same fallacious claims over and over again like you do. Appealing to the publications of Anon is an attempt at misdirection and trying to throw your mantle of idiocy off onto another
whatever pseudoscientific nonsense you think explains the biodiversity on this planet
unfortunately for you, jk, Anon (and the others) are backed by years of empirical data and education proving you are a few dandelions short of a peace movement... should re-read the links

just cause YOU don't understand doesn't mean we don't

JUST ANSWER ANON
is splicing responsible for all the genetic variation and diversity?
this is a yes or no answer
JVK
1 / 5 (1) Jun 04, 2014
...Anon (and the others) are backed by years of empirical data and education...


The study also shows that stickleback evolution is accelerated by the use of pre-existing genetic variation, instead of waiting for new, random mutations to arise, Wray explains.
http://www.nature...20120410

"If you learnt evolutionary biology and genetics a decade or more ago you need to be aware that those debates have moved on very considerably, as has the experimental and field work on which they are based." http://jp.physoc....abstract

"[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent.... Evolution was defined as "changes in gene frequencies in natural populations." The accumulation of genetic mutations was touted to be enough to change one species to another... Assumptions, made but not verified, were taught as fact." Mazur (2014)
Captain Stumpy
not rated yet Jun 04, 2014
@jvk
so... what you are saying is that IF you answer Anon, you will be poven an idiot with your own words again?
ANSWER THE QUESTION
Yes or no answer. It's very simple. You can't twist a yes or no answer.

Based on this quote from you:

Ecological adaptation is what we predicted, and that's what has been found, which makes our 1996 Hormones and Behavior review article relevant to everything else that's been published since then about alternative splicings that link the epigenetic landscape to the physical landscape of DNA in organisms from microbes to man.


is splicing responsible for all the genetic variation and diversity?

anonymous_9001
5 / 5 (1) Jun 04, 2014

The study also shows that stickleback evolution is accelerated by the use of pre-existing genetic variation, instead of waiting for new, random mutations to arise, Wray explains.
http://www.nature...20120410


Accelerated. Not exclusively due to. Regulation and modification of the genes (through mutation) work together.

With the other relevant part of cherry-picked quote:

"Regulatory changes could speed the stickleback's adaptation by controlling gene expression in multiple tissues with each mutation. The study also shows that stickleback evolution is accelerated by the use of pre-existing genetic variation, instead of waiting for new, random mutations to arise, Wray explains."

And again:

Based on this quote from you: ... is splicing responsible for all the genetic variation and diversity?
JVK
1 / 5 (1) Jun 04, 2014
Denis Noble: I would certainly go along with the view that gradual mutation followed by selection has not, as a matter of fact, been demonstrated to be necessarily a cause of speciation.
http://www.huffin...211.html

If anyone wants to argue with the president of the International Union of Physiological Sciences, they are welcome to do so by providing experimental evidence to support their claims. Until then, I will side with Dr. Noble and say: "If you learnt evolutionary biology and genetics a decade or more ago you need to be aware that those debates have moved on very considerably, as has the experimental and field work on which they are based." (p 1014)
http://jp.physoc....abstract

No one here seems to have ever learnt anything about evolutionary biology, which makes discussion with anonymous fools and idiot minions of biology teachers like PZ Myers a waste of time.
anonymous_9001
5 / 5 (1) Jun 05, 2014
There's a difference between saying it's not necessarily being a proximate cause of speciation and saying it doesn't contribute to geno- and phenotypic variation by producing novel DNA sequences.