Recap:
So, last time, I mentioned how DNA was transcribed into RNA that itself was translated into proteins. We also spend some time on how complementary nucleotide sequences bonded each others (if you are not familiar with the subject, go check it out, we will wait).
Role in gene regulation:
So, if you look at the second step of the central dogma, you can see the recently translated mRNA floating around, patiently waiting for the ribosomal complex to bind it and start transcribing it into protein…
Except that, at the last minute, a short RNA sweeps in and bind the mRNA instead. This block the binding site for the ribosomes and prevent the translation (that is called “RNA interference”).
Worse, viruses are the only organisms whose genome can sometime be found in the form of double stranded RNA so these structures are quickly targeted by dicer proteins that cut them into pieces.
This constitute a somewhat crude but a efficient mechanism to control the level of expression of a gene referred to as “posttranscriptional gene silencing”.
Bacterial CRISPRs:
A very cool application of RNA interference might be immunological.
There are sequences, present on most bacterial genomes, called (Clustered Regularly Interspaced Short Palindromic Repeats) that, when they were first discovered, nobody really understood what they did. Then somebody noticed that, at their center, was a short sequence that looked really like that of a bacteriophage (the term for any virus infecting bacteria).
At which point it was a small step to think that these CRISPRs might be involved in RNA interference with their matching sequence on the viral genome and, sure enough, it was quickly demonstrated that the presence of these sequence correlated with resistance against virus invasion. Moreover, knocking down these sequences rendered the previously resistant bacteria susceptible to infection.
It was a pretty cool find all by itself. But then, somebody decided to take a susceptible bacterial culture, infect it with a bacteriophage and look for survivors. Sure enough, a few bacteria did survive infection. Furthermore, when challenged again with the same virus, all the descendants from these survivors appeared resistant to the virus. At this point, looking back at the genome, the researcher noticed that the bacteria now harbored a shining new CRISPR region it didn’t before the infection, and this region did correspond to the sequence of the virus. In short, they had evidences suggesting that the bacteria, somehow, had been able to acquire part of the virus sequence and use it for protection. Technically, you could describe that as ‘acquired immunity’, if the term was not already taken.
In addition to this complementary DNA sequence, the CRISPRs are surrounded by a variety of sequences, termed Cas (for CRISPRs associated genes). These genes are extremely heterogeneous and code for a variety of proteins, more than 40 families of Cas have been described, several of which appear to be DICERS, molecules that specialize in cutting nucleotide sequences. Interestingly, Cas are very well distributed among the bacteria suggesting that a lot of horizontal transmission, gene passing between bacteria, is taking place.
The means through which these viral sequences are then integrate to the bacterial genome are not as of yet known. It is likely that some Cas are responsible, it might, for example, be an additional function of some of the DICERs…
Immunological role:
Interestingly, a mechanism, called RISC, had been discovered in eukaryote before, and it’s really cool:
So, here you have your strand of viral RNA, it’s either double stranded or it is single stranded, but will become, if briefly, at some point in the process of copying itself.
At any rate there is this protein floating around in the cytoplasm called a DICER (cool name, right? It’d make a great name for a super-hero. Or maybe one of these knives sold on TV infomercial). Anyway, the DICER’s job is to find and bind such a double stranded RNA and then, as its name suggest, it cut if off into pieces (ok, it would be an old school super-hero, like the Spectre but maybe he could have a team-up with the Punisher, or something). But the DICER’s job doesn’t stop there, it also pick up a small portion of the RNA strand that he just made a mess of.
Then the dicer bound by a molecule termed TRBP (for human immunodeficiency virus Transactivating Response RNA-Binding Protein) that apparently functions as a matchmaker, recruiting the Argonaute2 protein.
This second protein loads the RNA sequence into its groove. Then it destroys one of the strands and starts floating around in the cytoplasm, still carrying one strand of the RNA, now termed the “guide strand” the DICER-TRBP helped loading. This way, when it encounters a RNA sequence which is complementary from the guide strand, this complementary sequence (the “passenger strand”) will be bound and then cleaved and, in effect, the RISC acts as a molecular targeting system for the argonaute2 protein.
This mechanism presents some similarities with the one recently described for the CRISPRs. Furthermore, it is very well spread all over the eukaryotic kingdom, it is very common and im)portant in plants, but has also been described in humans. This suggests that it involved in a common ancestor, far away don’t the evolutionary tree. In fact, it is even quite possible that this ancestor was a bacteria and that the RISC system is but an evolutionary refinement of the good ol’ CRIPRs…
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