Yale Researchers Find New RNA Structures

Science Daily is reporting that researchers from Yale have discovered "very large RNA structures within previously unstudied bacteria that appear crucial to basic biological functions such as helping viruses infect cells or allowing genes to 'jump' to different parts of the chromosome." Ronald Breaker, professor of Molecular, Cellular, and Developmental Biology at Yale, stated that this would be equivalent to protein scientists finding a whole new class of enzymes. "The Breaker laboratory has used the explosion of DNA sequence information and new computer programs to discover six of the top twelve largest bacterial RNAs just in the last several years. One of the newly discovered RNAs, called GOLLD, is the third largest and most complex RNA discovered to date, and appears to be used by viruses that infect bacteria. Another large RNA revealed in the study, called HEARO, has a genetic structure that suggests it is part of a type of 'jumping gene' that can move to new locations in the bacterial chromosome."

Comments

RNA world

[Viol8]

This gives a bit of extra credence to the RNA world theory - ie that RNA was the precursor to DNA and very early life forms relied on it exclusively (yeah ok , some viruses still do but they're not technically alive) - if RNA can be used to do this as well as protein creation etc.

Re:RNA world

[Anonymous Coward]

If viruses are technically not alive, then what made the RNA world 'creatures' technically alive?
My vote is that life is not white and black like most things out here.
Viruses are closer to life than... most of the rocks we know.

Re:RNA world

[ColdWetDog]

Not necessarily - although I personally think that RNA was the earliest nucleic acid. This could have been a later evolutionary step or side step. It's a big world out there and we don't know jack... TFA (as weak as it is) doesn't tell us much. It could be an oddball messenger RNA or part of a ribonucleoprotein (like a ribosome).

Re:RNA world

[Anonymous Coward]

The problem with such strict almost arbitrary definitions of "alive" is what leads people to conclude that viruses are not alive. I find this absurd on many levels because we have time and time again been shown that the universe doesn't fit in nice little compartments we like to put things in.

They're not "lawmakers" they're legislators. They're not "viruses that infect bacteria" they're bacteriophages. Can the press stop dumbing down the language please? Oh Noes, heaven forbid it, someone might have to grab a dictionary once in a while! Quick, avoid this at all costs!! Dumb down everything!

Re:RNA world

[Gerafix]

The problem with your thinking is that most people would rather pick up Us Weekly than a dictionary. You really can't expect the masses to learn any scientific terms or concepts, especially when it's two whoppers for five bucks down at Burger King.

Re:RNA world

[sjames]

Metabolism. RNA vs. DNA isn't the distinguishing factor.

I do agree though that there is a gray area between alive and not alive.

Re:RNA world

[MightyMartian]

The problem is in the definition. In biology, there are plenty of concepts that are not binary (speciation is another tricky one). It's better to define life as a sliding scale than as a line in the sand. But this is nothing new. Since the discovery of symbiosis, and in particular parasitism, where we have organisms that may not have all the features of a fully independent living organism, it's been clear that you cannot define life in binary terms.

Re:RNA world

[fifedrum]

two whoppers for five bucks! AWESOME!

Re:RNA world

[Gerafix]

It is absolutely generalized but that doesn't mean it's wrong. Us Weekly has a much larger readership than that of Nature, for example. One simply has to look at the popularity of certain mythologies in the modern world to ascertain that science or the scientific method is not a significant part of many peoples lives (even if their daily life depends on science). This is of course blatantly obvious.

Perhaps picking on the burgers was unnecessary but the whole industry does survive on the rather insidious instant gratification by consumption of fatty salty food that exists solely by peoples carelessness or ignorance of what it does to their bodies. Well, that and it's cheap in the short run.

Not to mention that basic biology is hardly a specialty, anybody with a half-assed high school education should be able to at least follow most of what is on Slashdot. Well... unless you've had an American education ba-dum-dum-ch. How's that for generalization!

Curious choice of analogies

[Red Flayer]

Ronald Breaker, professor of Molecular, Cellular, and Developmental Biology at Yale stated that this would be equivalent to protein scientists finding a whole new class of enzymes.

Thanks. That enzyme analogy is really helpful to people in the bio research field.

But this is slashdot. We expect more from our analogists. Specifically, we expect a car analogy (no, a pizza analogy does not suffice).

Perhaps discovering this new class of RNA structures is like discovering a new type of fuel injection system, so we better optimize fuel-air mixture for power and efficiency. Perhaps it's like discovering a new type of rubber for our tires, for better traction and wear. Perhaps it's like discovering a new type of battery so we can all get cheap, quickly charging, long-range electrical cars.

But most likely it's not like any of those things, and we'll never really understand the implications of this discovery, because the people who really understand it didn't bother to give us the necessary car analogy.

Bastards.

Re:Curious choice of analogies

[Nadaka]

Its like this. There are trucks, and there are station wagons. Then all of a sudden you discover a new type of vehicle called an SUV that is a station wagon, but it looks like truck.

Re:Curious choice of analogies

[ColdWetDog]

Here, let me help. This brief blurb discusses Dr. Breaker's research history a bit better and shows where this current research stems from. He is a proponent of the "RNA World" hypothesis and actually has done some seminal research in the field.

Back to the car.... Hmmm.... OK - the RNA World hypothesis states that the first nucleic acid (the chemical responsible to for transmitting genetic information) was RNA. Breaker's hypothesis is that if that is the case, one should find RNA-based control structures somewhere since they are ancestral and nature loves to preserve ancestral things (don't recreate the wheel very often and if you do, keep a copy of the old wheel stashed somewhere).

He did find evidence of this in the coenzyme that helps vitamin B12 activity (see the previous link). So, perhaps these new RNA molecules have some sort of control function.

So, it's like finding a whole class of levers and rods that allow your car to do things when you were expecting that buttons and switches did all of the work.

Does that help?

Re:Curious choice of analogies

[MightyMartian]

The first thing that people have to overcome when studying evolution is the notion that evolution somehow works towards some sort of perfection. Evolution just as often, or more often, creates "good enough" solutions, and is often highly conservative once such solutions are found. While RNA is a far less efficient and even stable molecule than DNA, that says nothing as to its potential aka the RNA world hypothesis. RNA might not be the best moleculr out there (heck, DNA probably isn't either), but at some stage, it was good enough.

Yale Evolution and Behaviour Lectures

[mindbrane]

I'm nearly finished the Yale lectures on evolution, ecology and behavior. Professor Stearns addresses the RNA world theory of life origins. The Yale lecture series is really outstanding. If you're a Global Warming skeptic you'll be interested in Professor Stearns suggestion that human induced global warming has the potential for an extinction event on par with the one that drove the extinction of the dinosaurs. The production values in the Yale lectures is really good and the lectures offered give a sort of pocket edition of the human condition.

Re:Yale Evolution and Behaviour Lectures

[Anonymous Coward]

One of the main reasons I don't believe in the man-induced climate change theory is that it comes from the same group of scientists who've allowed themselves to interpret data in support of evolution vs creation. If they are so screwed up on that, they probably are on the climate change thing as well.

Re:Yale Evolution and Behaviour Lectures

[MightyMartian]

One of the main reasons I don't believe in the man-induced climate change theory is that it comes from the same group of scientists who've allowed themselves to interpret data in support of evolution vs creation. If they are so screwed up on that, they probably are on the climate change thing as well.

I nominate this extraordinary bit of rubbish for Non Sequitur of the Year. I'd like to think it's a bit of satire, if for no other reason than I need to believe in the fundamental decency and intellectual rigor of humanity.

Re:Yale Evolution and Behaviour Lectures

[MightyMartian]

Global warming pseudo-skeptics are a lot like a kid throwing lit matches in their livingroom, insisting the fires are quite natural and have no correllation with the flaming sticks he's tossing around.

Re:Yale Evolution and Behaviour Lectures

[radtea]

You do realize that a lot of glaciers and polar caps are melting?

Pointing out that X, which is predicted by AGW models, is happening, does not change the fact that Y, which is also predicted by AGW models, is not happening.

So your point in no way addresses my observation (I am the GP above--dunno how it came out A/C'd) that the evidence is mixed. Just like the observation that the possible consequences of AGW are dire, the observation that some evidence is consistent with AGW predictions fails to address the sceptic's point, which is that there are significant pieces of evidence that do not match AGW predictions, and that the range of AGW predictions is sufficiently broad that you can find a prediction for most phenomena, including local cooling.

That's all well and good, but AGW proponents cannot point to the cases where the data are consistent with relatively robust predictions and say, "This proves AGW is happening" while at the same time ignoring data--like the local temperature records I mention above--that is inconsistent with similar predictions and say, "This does not disprove AGW is happening."

That is, the seriousness with which AGW proponents and deniers take any particular data set is entirely dependent on how well is supports their preferred outcome.

An honest sceptic will point out both the data on both sides, as I did. Replying to such a sceptic with a rhetorical question regarding one particular piece of data on your favoured side simply adds noise to the debate without meaningfully furthering it.

To further the debate we need more data, better models and more open and accessible data and models: given the huge public policy implications of climate science, the climate science community has an absolute obligation to make all of their raw data and metadata available to everyone. Anything else and there will be a justified suspicion that the data are being massaged or used selectively for political purposes.

Regardless of which side of the debate you're on, if you're interested in the science you must be in favour of this kind of open process.

From the original Nature article...

[Guppy]

From the published article in Nature:

In Lactobacillus brevis ATCC 367 and other organisms, GOLLD RNA resides in an apparent prophage. We therefore monitored GOLLD RNA transcription in L. brevis cultures grown with mitomycin C, an antibiotic that commonly induces prophages to lyse their hosts22. Increased GOLLD RNA expression correlates with bacteriophage particle production, and DNA corresponding to the GOLLD RNA gene is packaged into phage particles

The role of GOLLD RNA is uncertain enough, and the GOLLD-virus relationship close enough, that it might be reasonable to suggest that they have not found a new RNA structure in bacteria, but a new class of RNA structure in a virus (which is odd enough it may give us a new group of viruses). Since these bacteria are uncultured or only recently cultured, they are poorly characterized, we might not really have a good idea of whether there is some "normal" type of this bacteria that is free of the RNA structure, and that the structure is merely an artifact of being infected.

Of course, given how messy host-virus relationships can be, it's entirely possible you could have a species of bacteria universally infected by this jumbo-RNA-producing virus, or that they might have reached some sort of symbiosis, with GOLLD playing some role beneficial to the host. Likewise, while HEARO hasn't been associated with a prophage, it's role in moving in and out of the genome could suggest it was introduced by a phage at some point in the past, and has since acquired an identity and role in the host of it's own.

Re:From the original Nature article...

[HiChris!]

This was along the lines of my first thought. These large RNAs could just be leftover from some sort of viral infection. Especially considering viral genes can jump in and out of the genome depending on the phase of infections. This could be analogous to the idea that the mitochondria and chloroplast were small bacteria like organisms that were engulfed by a larger cell and then became symbiotic. These large RNAs could be providing some sort of biological advantage and have become "part" of the organism.

Re:From the original Nature article...

[jstomel]

"Very large" compared to other non-coding non-ribosomal functional RNAs. As a biologist I would generally classify the ribosomal RNAs as huge. At 1000 nucleotides it's bigger than most protein complexes.

Re:From the original Nature article...

[Rich0]

It amazes me just how much of a hack life seems to be at times. Stuff like this doesn't surprise me at all any more.

I began to realize how much of a hack life was when I first learned about HOK and SOK. It is a remarkably simple and brutally efficient way of keeping a plasmid around - if it weren't for the fact that the plasmid actually has some benefits it would be the ultimate selfish gene. :)

Move definition up

[SnarfQuest]

From the article: (Move definition up) RNA molecules are best known for carrying information from genes encoded in DNA to ribosomes

Are there (Move definition down) RNA molecules too?

Do these articles use the same editors as slashdot?

Pah!

[ThatsNotPudding]

According the Dr. Hubert J. Farnsworth, the R stands for Robot!