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Yale Researchers Find New RNA Structures 90

Posted by ScuttleMonkey from the micro-steps-for-mankind dept.
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."
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Yale Researchers Find New RNA Structures More

Yale Researchers Find New RNA Structures

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  • RNA world (Score:5, Interesting)

    by Viol8 ( 599362 ) on Monday December 07, 2009 @12:08PM (#30354864) Homepage

    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: (Score:2, Insightful)

      by 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: (Score:3, Insightful)

        by sjames ( 1099 )

        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 (Score:5, Insightful)

        by MightyMartian ( 840721 ) on Monday December 07, 2009 @01:11PM (#30355652) Journal

        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: (Score:2)

        by Viol8 ( 599362 )

        Viruses require more complicated biological systems to reproduce themselves. This is hardly going to be how the earliest RNA life reproduced if it was the most complex life around at the time.

      • Re: (Score:1)

        by markian ( 745705 )

        If viruses are technically not alive, then what made the RNA world 'creatures' technically alive?

        well, they're not technically dead either...

    • Re: (Score:1, Insightful)

      by 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.

      • Re: (Score:2, Interesting)

        by 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: (Score:3, Insightful)

          by Gerafix ( 1028986 )
          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 (Score:4, Funny)

            by fifedrum ( 611338 ) on Monday December 07, 2009 @01:15PM (#30355698) Journal

            two whoppers for five bucks! AWESOME!

          • Exactly why I advocate adopting a monetary system in base 7.

            • Exactly why I advocate adopting a monetary system in base 7.

              That would be for use on Mondays, Wednesdays and alternating Fridays? Decimal for Tuesdays, Thursdays and the other Fridays. And for the nostalgic amongst us, bring back duodecimal on weekends.

    • Re:RNA world (Score:5, Interesting)

      by ColdWetDog ( 752185 ) on Monday December 07, 2009 @12:20PM (#30355018) Homepage
      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).

    • "This gives a bit of extra.. "

      what exactly in the article do you mean by "this"?

    • our very distant ancestors were also, at some point, "not technically alive". What would prevent them from relying on the same tricks ?

  • Curious choice of analogies (Score:5, Funny)

    by Red Flayer ( 890720 ) on Monday December 07, 2009 @12:15PM (#30354968) Journal

    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 (Score:4, Funny)

      by Nadaka ( 224565 ) on Monday December 07, 2009 @12:28PM (#30355134)

      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.

      • 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.

        Just like a big series of internets.

      • Seriously - they are much closer, just a lil longer hood, and some higher, more unstable wheels for all that "off roading" that the SUVs do.

        • Re: (Score:1)

          by snadrus ( 930168 )
          After all, "off roading" depends on top-heavy design.
          • That's why they invented the "crossover". In the domain of offroading, a crossover is a mix between a truck and something designed to have the wheels on top.

    • Re:Curious choice of analogies (Score:5, Insightful)

      by ColdWetDog ( 752185 ) on Monday December 07, 2009 @12:31PM (#30355166) Homepage
      Here, let me help. This brief blurb [acs.org] 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" [rockefeller.edu] 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?

      • 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.

        So what you're really saying is it's like finding out that the latest MP3-playing, 8-speaker stereo-containing car has an 8-track hidden under the spare tire.

        ...yay?

        • Re: (Score:2)

          by ardle ( 523599 )
          I remember meeting someone whose "typical" immune system didn't work properly but who was able to function pretty well with the help of an "older" one. I don't know biology but assume this is more of the same?
      • These car analogies break down because they describe new design ideas. The summary makes it sound more like a mechanic opening the hood to do an oil change and seeing a new kind of engine that's not described anywhere, that apparently lots of people have had in their cars for thousands of years.
        • Guys ... Although it may seem contrary to folks who grew up in the US, automobiles do not encompass the entirety of human thought and accomplishment. Thus, not everything fits comfortably within the narrow confines of a car analogy. It's like some things are cars and then there is pizza.

          Got it?

          • Pizza, isn't that simply "food delivered by car" ?

          • Next you'll be telling me that we should read the articles before commenting. Pshaw!

          • Thus, not everything fits comfortably within the narrow confines of a car analogy.

            Heresy.

            There is nothing that cannot be explained via use of a car analogy. There are no narrow confines... car analogies are infinite in their applicability.

            I defy you to give me one example of a situation not analagous to something in a car, the car industry, or related behavior (of course, it would have to be a subject I'm familiar with in order for me to make an accurate car analogy).

            • Re: (Score:2)

              by dissy ( 172727 )

              Making a good car analogy is a lot like taking the scenic route instead of the direct route in your car. Sure it takes more gas, but the laughs and memories will be yours for a lifetime!

              PS, I think you left your parking break down...

    • It's like researchers discovered a gun powder fired internal combustion engine. We've long suspected that such a thing is theoretically possible, some people even speculate that the first ICE's invented were gun powder fired, but no one has ever seen one working in real life. Furthermore, it's massively innefficient by todays standards so what uses it may have are hard to see.

      • Re:Curious choice of analogies (Score:5, Informative)

        by MightyMartian ( 840721 ) on Monday December 07, 2009 @01:55PM (#30356194) Journal

        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.

        • Re: (Score:2)

          by MarkvW ( 1037596 )

          That's stupid. Evolution doesn't create solutions to anything. Evolution just describes what happens--it isn't an animated event for God's sake.

          • Would using the term "evolutionary process" make you feel better? As it is, biologists quite often refer to "evolution" as an active process. I don't see the point to your semantic argument here, other than that you have nothing particularly useful to say, but still want to appear as if your smart.

            Grammar/semantic flames, like spelling flames, are for low-grade intellects with too much time on their hands. Go masturbate or play WoW with a pencil up your ass. It'll be better for everyone.

          • Biological evolution "strives to solve" one problem, how to replicate and survive. There are many solutions to this problem, even if /.ers fail at one of them ;>)

    • Perhaps it's like discovering a new type of Pepperon-

      Oh.

    • Re: (Score:2)

      by zx75 ( 304335 )

      It's like finding a whole new wing of the Library of Congress.

      Happy?

    • Actually, it's more like discovering a new shade of blue that you could theoretically color your car but won't because it looks horribly old-fashioned.

  • Yale Evolution and Behaviour Lectures (Score:5, Interesting)

    by mindbrane ( 1548037 ) on Monday December 07, 2009 @12:17PM (#30354986) Journal
    I'm nearly finished the Yale lectures on evolution, ecology and behavior [yale.edu]. 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: (Score:3, Funny)

      by 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 (Score:4, Insightful)

        by MightyMartian ( 840721 ) on Monday December 07, 2009 @01:15PM (#30355696) Journal

        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.

  • From the original Nature article... (Score:5, Interesting)

    by Guppy ( 12314 ) on Monday December 07, 2009 @12:42PM (#30355298)

    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: (Score:2, Interesting)

      by HiChris! ( 999553 )
      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 organis

    • Re: (Score:1, Funny)

      by Anonymous Coward

      So does this explain the recent rise in the value of GOLLD?

    • I wonder why Science Daily qualified them as "very large", only to note later that "One of the newly discovered RNAs, called GOLLD, is the third largest and most complex RNA discovered to date"

      According to Figure 1 from Nature article, it's less than 1000 nucleotides and significantly smaller than ribosomal 16S (which has structure as well). I work with those RNA on computational side and none of the biologists ever referred to them as "very large".

      "Very large" compared to what?

      • Re:From the original Nature article... (Score:4, Informative)

        by jstomel ( 985001 ) on Monday December 07, 2009 @01:33PM (#30355928)
        "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.
        • That would assume that these large RNAs are non-coding functional RNAs, something not clearly answered one way or the other by the paper. One possiblity is that these RNAs are remanants of viruses that have integrated into the bacteria (indeed the fact that the GOLLD RNA resides in an apparent prophage and is expressed under conditions that promote prophage expression supports this conclusion). Then it might be more appropriate to compare the size to viral genomes which can also be very large, highly stru

      • Re: (Score:2)

        by mea37 ( 1201159 )

        'qualified them as "very large", only to note later that "One of the newly discovered RNAs, called GOLLD, is the third largest and most complex RNA discovered to date"'

        I'm not seeing what's wrong with that.

        The third tallest building in the world [infoplease.com] is 101 stories / 1614 feet tall. That's a very large building.

        I guess you were assuming that "very large" meant "larger than any similar thing we'd seen before"; but to me "significantly larger than typical thigns of the same type" is very large.

        • There are millions of buildings in the world vs few types of RNA.

          Did you look at the Fig.1 in the Nature article? New "very large" RNA are right in the middle of the range of sizes.

    • Re: (Score:3, Insightful)

      by Rich0 ( 548339 )

      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 [wikipedia.org]. 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 (Score:3, Funny)

    by SnarfQuest ( 469614 ) on Monday December 07, 2009 @01:18PM (#30355724)

    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?

  • Are these new RNA structures, or newly discovered RNA structures? My bet is that they are ancient structures that these guys have just recently found.

    • The word "discovered" in the first fucking line of the summary may provide a hint.

      As would the smallest amount of common sense.

  • Pah! (Score:2, Funny)

    by ThatsNotPudding ( 1045640 )
    According the Dr. Hubert J. Farnsworth, the R stands for Robot!
  • 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. Well, at least they've nailed their analogies! Now I can finally relate to their situation.

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