On coupling

No, not that sort of coupling.

I was writing up today’s Faculty Dailies, catching up on (yet) another paper about how ribosomes control the rate of transcription.

As has been known for decades, bacterial transcription and translation are tightly coupled. What’s interesting about the recent work is that the presence/processivity of the ribosome appears to feedback on the rate of transcription by stopping the RNA polymerase from going backwards. (I can’t help but think there’s also a link between this phenomenon and the observation that rare codons slow translation, but that’s something else to worry about.)

Now, when I was working on nuclear trafficking I managed to get our lab’s website into the first page of Google hits for that term (about third, I think). That’s irrelevant: what is relevant is that I left the field nearly five years ago, and at that time we all assumed that, just as in bacteria, translation and transcription were tightly coupled in eukaryotes. How can this be, seeing as they’re in separate compartments? Well, we figured that the messenger RNA was being exported through nuclear pores while the arse-end was still being transcribed. All the RNA-binding proteins seemed to interact with enough of each other that we could happily hypothesize a continuum from chromatin through RNA polymerase through the splicing machinery to the nuclear pore.

Besides, we couldn’t figure out what made mRNA go in one direction through the pore (i.e., out)–although we were pretty certain that it was ribosomes clamping down on the mRNA as it poked out of the nuclear pore, stopping it going back in, and equilibrium dynamics doing the rest (in much the same way this paper postulates that preventing back-tracking is how ribosomes control RNA polymerase)–so this made intuitive sense and seemed to answer a lot of awkward questions. The actual mechanics were simply a matter of time, we figured.

So, coming back to this morning, I was a little surprised to find the sentence

In contrast to bacteria, transcription and translation in eukaryotes take place in different cellular compartments and are not coupled

in a “Research Highlight”:http://www.nature.com/nrg/journal/v11/n6/full/nrg2803.html in Nature Reviews Genetics.

Um, has the field done a complete volte-face while I was noodling away at zinc fingers and websites? Were we wildly ahead of our time, or just completely wrong? What is the latest thinking on this? Anybody got a Stryer?

About rpg

Scientist, poet, gadfly
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2 Responses to On coupling

  1. vishal kalel says:

    great post Richard.
    about Stryer, I think it takes some decades before things come into conventional text-books. Latest things should not come into text-books immediately, since years of rigorous validation is required to establish a concept kicking away major flaws!
    so there is no other option but to keep reading new papers and forming our own opinions, no matter anybody accepts it or not!
    If all think alike, maybe no-one is thinking! (I didn’t say that..)
    I was not sure what to do today, but your post has made my day..
    (more precisely Birthday! )
    Gonna read more about such papers today while sipping my favorite red wine..

  2. Richard P. Grant says:

    Heh! Happy birthday Vishal! Glad you like my present 😉
    Textbooks, especially in biochemistry/mol-cell biology I think, are actually pretty current. At least, when I was reading them everyday it seemed that they were citing papers only a couple of years old. And naturally, we did experiments and read papers that showed that the textbooks were wrong; but they were state of the art at the time. It’s the nature of the beast. Textbooks are a useful historical resource to see what we believed last year, maybe, but that’s a post for another day.

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