MDR: Multi Drug Resistance Protein. It's an ABC (ATPase Box Cassette) Transporter. In other words, this gene encodes an energy utilizing pump that sits on the plasma membrane and actively transports (mostly hydrophobic?) compounds out of the cell. As I wrote yesterday, a silent change in this gene at the nucleotide level alters the transporter's specificity. According to a paper in the Jan 26th edition of Science, the altered MDR protein is just fine at transporting most compounds but is defective in the transport of a particular compound. The silent mutation does not affect mRNA levels or protein levels, so the change has nothing to do with how much of the gene product is produced.
So what's going on?
Just like that other paper from late last year, silent mutations may regulate how quickly a transcript is translated and translation rates may affect protein folding. Last time the mutation was thought to affect RNA folding and thus affect how fast the ribosome reads through a particular segment of the gene (and thus affect local folding patterns), here the authors suggest that the silent mutation introduces a relatively rare codon which would act similarly to slowdown the ribosome. To test this idea, the authors measure the protein's sensitivity to trypsin digestion. And yes, the MDR variant gets digested more quickly than the wildtype MDR version indicating that the protein folding may be slightly different.
But honestly now, to prove beyond a reasonable doubt this idea that certain "silent mutations"="changes in protein folding", someone out there should find the structure of the two protein versions. Since the versions of MDR-1 studied in this paper are mammalian membrane-bound proteins (and members of the ABC transporters) this ain't going to happen anytime soon.
And here's another interesting issue, because this MDR variant occurs naturally within the human population and because MDR is responsible for pumping out many hydrophobic compounds out of cells, this study has big implications for therapeutics. Although our MDR proteins may be the same sequence wise, my cells may not pump out certain compounds that your cells pump out with ease. For more on this paper, see Quitter's post.
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To be fair, they had more evidence than just trypsin digestion. The function was altered and a conformation-specific antibody also failed to recognize the transcript variant.
The reason I find this immensely believable (even without the NMR/crystal data) is that why else would we end up with codon preference issues? I think it explains codon preference very nicely, and allows the cell an extra layer of complexity and control over protein function. If true these results mean that the code being "degenerate" is a misnomer. In reality the codon preference transmits a kinetic piece of information as well as the coding information allowing a greater variety of protein folds to occur.
I really like this result. I think it explains a lot, and the evidence for it is pretty tight so far. Not that a lot of exciting stuff in Science doesn't turn out wrong, but this seems to make so much sense.
I think the paper was a really awesome one. One of the most interesting papers that I have seen in recent times and again trypsin digestion is such a coarse grained technique that it would be hard for two structures to give different banding patterns unless there is proabably a real difference. Come on Alex! We all know how hard getting a crystal structure or NMR would be for the smallest of proteins and its a stretch to ask them to do every test on the planet to make their claim. :-)
In other words, codon usage and thus translation rate at various points within the mRNA may optimize to promote the correct folding. I guess. There are certain genes that are full of rare codons - perhaps these tracks are simply ribosome stalling devices.
As for why others at scienceblogs haven't commented ... most of the other scienceblogs deal with higher level biology and/or computational biology. Pharyngula is a developmental biologist, the most he ever covers at the subcellular level is signalling. Coturnix does not deal with pure cell biology, let alone molecules. RPM covers genetics. Sandra Porter computational/genomics. Razib, genetics ...
Well it would provide conclusive proof. The bigger the idea, the higher the burden of proof. It's not that I don't believe it, but the results may rely on someother unknown factor. Look I'm not asking that this group should have performed NMR but in the end I'd like to see the change in the structure to be absolutely sure.
They also mutated the rare codon to the isoleucine codon ATA and checked that this codon (also rare) produced a variant with even larger decreases in inhibitor effects. These ideas of codon usage changing folding are not new. I summarized some related work on a blog post.