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Proteins are defying textbooks

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We bet this isn’t the only time they have done so. 😉

Here, from U Utah Healthcare:

Open any introductory biology textbook and one of the first things you’ll learn is that our DNA spells out the instructions for making proteins, tiny machines that do much of the work in our body’s cells. Results from a study published on Jan. 2 in Science defy textbook science, showing for the first time that the building blocks of a protein, called amino acids, can be assembled without blueprints – DNA and an intermediate template called messenger RNA (mRNA). A team of researchers has observed a case in which another protein specifies which amino acids are added.

“This surprising discovery reflects how incomplete our understanding of biology is,” says first author Peter Shen, Ph.D., a postdoctoral fellow in biochemistry at the University of Utah. “Nature is capable of more than we realize.”

To put the new finding into perspective, it might help to think of the cell as a well-run factory. Ribosomes are machines on a protein assembly line, linking together amino acids in an order specified by the genetic code. When something goes wrong, the ribosome can stall, and a quality control crew is summoned to the site. To clean up the mess, the ribosome is disassembled, the blueprint is discarded, and the partly made protein is recycled.

Yet this study reveals a surprising role for one member of the quality control team, a protein conserved from yeast to man named Rqc2. More.

But what is this about “Nature is capable of more than we realize”? Does nature have a mind that has a search space for solutions?

Like a half-made car with extra horns and wheels tacked to one end, a truncated protein with an apparently random sequence of alanines and threonines looks strange, and probably doesn’t work normally. But the nonsensical sequence likely serves specific purposes. The code could signal that the partial protein must be destroyed, or it could be part of a test to see whether the ribosome is working properly. Evidence suggests that either or both of these processes could be faulty in neurodegenerative diseases such as Alzheimer’s, Amyotrophic lateral sclerosis (ALS), or Huntington’s.

“There are many interesting implications of this work and none of them would have been possible if we didn’t follow our curiosity,” says Brandman. “The primary driver of discovery has been exploring what you see, and that’s what we did. There will never be a substitute for that.”

Are these people trying to say, don’t fire us because we find evidence for design in nature?

If so, let’s hope they are not forced to yelp some fake disclaimer at a press conference.

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Comments
AVS: I am not a lawyer, but certainly you are one who does not want to understand. The "random sequence of alanines and threonines" is a signal, and it conveys information. But the information is always the same. It is information about the state of the protein (failed). It is information that has function only because it is recognized in the system by something else (that's why I call it a "signal"). On the other hand, the specific sequence in each protein is functional because it confers a specific biochemical configuration and activity, which is different for each protein. mRNA conveys specific information for its protein, deriving it from the protein gene. Rqc2 does nothing like that. It marks different defective proteins with the same signal: "defective". Is that the same thing for you? mahuna seemed to believe that the Rqc2 protein assembled specific proteins and conveyed the information for their sequence, like mRNA. I have only tried to correct that misunderstanding. However, maybe I can apply for law school, after all... :)gpuccio
January 7, 2015
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So no information, except for the signal, and the signal is a random sequence of alanines and threonines. How can you say there is no sequence information then? Your argument sounds like doublespeak to me, are you a lawyer?AVS
January 7, 2015
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Dionisio: Ah, the "condition" seems to be "stalled translation", but it is not clear how that recruits the protein and its action.gpuccio
January 7, 2015
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Dionisio: The paper is not free, so I have no access to details. However, if you look at the picture in the reviewing article, it seems that the protein links the tRNAs for alanine and threonine, and then binds the ribosome and adds those aminoacids to the incomplete protein. IOWs, it acts like a mRNA, but has no specific sequence information, and can add only alanine and threonine.gpuccio
January 7, 2015
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AVS: "So Gpuc, a signal that says “this is a defective protein,” doesn’t qualify as information?" My statement was: "So, no specific information added here by the protein, except for a “signal” that means: this is a defective protein." Emphasis added. The meaning is rather obvious: No information specific to generate a functional sequence is provided, but information is added in the form of a signal that the protein is not working. The signal is always the same (a random tail of alanine and threonine), and has a functional meaning (it marks the protein and its state), but is not a specific functional sequence for that specific protein. IOWs, it is not a substitute of mRNA, as mahuna seemed to believe. Satisfied?gpuccio
January 7, 2015
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I was not mistaken https://uncommondescent.com/intelligent-design/jonathan-wells-far-from-being-all-powerful-dna-does-not-wholly-determine-biological-form/ The new research
A team of researchers has observed a case in which another protein specifies which amino acids are added.
Dr. Wells
Even after RNAs are translated into proteins, the latter change in ways that cannot be traced back to DNA sequences.
Andre
January 6, 2015
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So Gpuc, a signal that says "this is a defective protein," doesn't qualify as information?AVS
January 6, 2015
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So, no specific information added here by the protein, except for a “signal” that means: this is a defective protein. So, proteins remain incapable of generating sequence information, but they can certainly add functional signals, which can be recognized in a complex, integrated system. Not good for “proteins first” OOL theories. Very good for ID.
As usually, gpuccio clarifies the problem for the confused interlocutors and the rest of us. :) However, I have a question about this part of the text:
Before the incomplete protein is recycled, Rqc2 prompts the ribosomes to add just two amino acids (of a total of 20) – alanine and threonine – over and over, and in any order.r
How does Rqc2 do the 'prompting' ? Under what conditions?Dionisio
January 6, 2015
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I think you are probably mistaken, Andre. Citation?wd400
January 6, 2015
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If I'm not mistaken, I think this is exactly what Dr. Wells predicted.Andre
January 6, 2015
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mahuna: I am afraid that this paper is no great help for protein first theories of OOL. The protein, Rqc2 (about 1000 AAs long), "simply" adds random sequences of two AAs (Alanine and Threonine) at the carboxy-terminal end of an incomplete protein in cases of "stalled translation". The abstract:
In Eukarya, stalled translation induces 40S dissociation and recruitment of the ribosome quality control complex (RQC) to the 60S subunit, which mediates nascent chain degradation. Here we report cryo–electron microscopy structures revealing that the RQC components Rqc2p (YPL009C/Tae2) and Ltn1p (YMR247C/Rkr1) bind to the 60S subunit at sites exposed after 40S dissociation, placing the Ltn1p RING (Really Interesting New Gene) domain near the exit channel and Rqc2p over the P-site transfer RNA (tRNA). We further demonstrate that Rqc2p recruits alanine- and threonine-charged tRNA to the A site and directs the elongation of nascent chains independently of mRNA or 40S subunits. Our work uncovers an unexpected mechanism of protein synthesis, in which a protein—not an mRNA—determines tRNA recruitment and the tagging of nascent chains with carboxy-terminal Ala and Thr extensions (“CAT tails”).
And from the article: "Yet this study reveals a surprising role for one member of the quality control team, a protein conserved from yeast to man named Rqc2. Before the incomplete protein is recycled, Rqc2 prompts the ribosomes to add just two amino acids (of a total of 20) – alanine and threonine - over and over, and in any order. Think of an auto assembly line that keeps going despite having lost its instructions. It picks up what it can and slaps it on: horn-wheel-wheel-horn-wheel-wheel-wheel-wheel-horn." Emphasis mine. And: "Like a half-made car with extra horns and wheels tacked to one end, a truncated protein with an apparently random sequence of alanines and threonines looks strange, and probably doesn’t work normally. But the nonsensical sequence likely serves specific purposes. The code could signal that the partial protein must be destroyed, or it could be part of a test to see whether the ribosome is working properly. Evidence suggests that either or both of these processes could be faulty in neurodegenerative diseases such as Alzheimer’s, Amyotrophic lateral sclerosis (ALS), or Huntington’s." Again, emphasis mine. So, no specific information added here by the protein, except for a "signal" that means: this is a defective protein. So, proteins remain incapable of generating sequence information, but they can certainly add functional signals, which can be recognized in a complex, integrated system. Not good for "proteins first" OOL theories. Very good for ID.gpuccio
January 6, 2015
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I've looked at this article. The title is fairly over-hyped. From what I remember, they are some actual proteins that work with the mRNA to add one or several amino acids to the end of the string, usually when there is a problem of transcription. So you have "proteins" recruiting t-RNAs. IIRC, this is linked to an elimination system in the cell which destroys defective proteins. It is something completely beyond the central theory of molecular biology, but not as radical as the cover article makes you think. Nevertheless, population genetics takes another blow, though slight.PaV
January 6, 2015
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On the one hand, Design in Nature is incredibly obvious. And on the other hand, incredibly deniable. Scientifically obvious and scientifically deniable. Why would Design be so obvious and yet so deniable?ppolish
January 6, 2015
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Its soup not slop, Mahuna. Soup is designed, slop is not:) "Soup" and "souping up" (noun/verb) are design metaphors. Fine tuned both.ppolish
January 6, 2015
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Um, I wouldn't start celebrating another Intelligent Design victory. You just admitted that amino acids can be assembled into genes without DNA or RNA existing first. I think this gives new life to the primordial soup. Of course we may simply be pushing the lump down the python. How did the first protein form, before it began assembling other proteins from raw amino acids? I mean, cells are formed by other cells, which are formed by genes which are formed by DNA which are formed by RNA which can be formed by proteins which are formed from amino acids, which are formed by... Cells? I'm also guessing that "assembler proteins" can each only assemble 1 type of protein, which again means that there is Information embedded in the protein. And the Information got there... how?mahuna
January 6, 2015
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