Might this apply?

A recent article in RNA – “The exozyme model: A continuum of functionally distinct complexes” – provides at once a timely review of exosome structure and function, and an interesting hypothesis that attempts to explain some interesting features of the exosome as it is found in different eukaryotes.

Recall that the exosome is the term for a (THE) RNA degrading machine in eukaryotes, and that it is analogous in many ways to the degradosome in bacteria.  Over the years, various and sundry exosome subunits have been implicated by genetics or biochemistry in numerous RNA processing and degrading events or systems.  However, there are differences, in terms of subunit composition and activity, between different organisms.  Because of these differences (that I won’t list here – Kiss and Andrulis do an excellent job that would take thousands of words to summarize), the authors of the cited review propose that the “exosome” is better thought of as a collection of “exozymes”, all of which share some subset of the subunits that collectively are usually associated with the conceptual exosome. In the authors’ own words:

“1. Exozymes are composed of exosome subunits either alone or as a mélange of exosome subunits, exosome cofactors, and non-exosome polypeptides.

2. Exozymes range in size from one component to many components with the traditional core exosome and associated cofactors representing the largest exozymes.

3. Smaller exozymes may be dissociated from the core exosome, or they may maintain dynamic relationships with the core and other exosome subunits.

4. Exozymes should be subcellularly compartmentalized and have metabolic pathway-restricted substrates.

5. Exozyme complexes are predicted to function independently of other exozymes via different substrate specificities, or they may share RNA substrates by participating in the same or different steps of RNA processing.

6. Exozymes are predicted to have some non-RNA metabolic functions.”

There is much to like about this concept, but what really intrigues me is how easily the concept applies to the plant polyadenylation complex as well.  Many of the same sorts of evidence that leads Kiss and Andrulis to the exozyme model also exists in the case of the polyadenylation complex.  I have briefly discussed one provocative finding, showing that Giardia lamblia seems to lack about 4/5ths of the subunits seen in the mammalian and yeast polaydenylation complexes.  My lab has published other findings that suggest that different tissues in plants may possess somewhat different polyadenylation complexes.  The possibility that polyadenylation in plants may involve collections of somewhat distinctive subcomplexes has been broached here, as well.

Does the exozyme model apply to the plant polyadenylation complex?  Who knows.  But the model is a fascinating framework that can guide future work.

The “Exozyme” citation:

DL Kiss, ED Andrulis. The exozyme model: A continuum of functionally distinct complexes. RNA 17: 1-13. 2011.

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3 Responses to Might this apply?

  1. Steve Mount says:

    I haven’t read the Kiss and Andrulis article yet, but I thought I’d share my concern that when considering comparative genomics data from organisms as divergent as Giardia, you have to bear in mind the possibility of nonhomologous replacement, a phenomenon that occurs so rarely for the machinery of gene expression that we tend to forget about it. That said, their concept does sound like something that might have broad application to RNA processing (and perhaps beyond).

  2. Arthur Hunt says:

    Hi Steve,

    I agree that nonhomologous replacement is an interesting and quite viable possibility when it comes to the polyadenylation complex. I think this phenomenon may add more possibilities to the exozyme model. Instead of thinking of just subcomplexes of various combinations of core or conserved subunits, one might consider subcomplexes where some core subunits are functionally replaced by an otherwise unrecognizable protein.

    A vague and abbreviated literature that hints at such a possibility when it comes to CPSF30 leaps immediately into my mind – probably because this subunit occupies lots of my writing time lately.

  3. […] confirmed the exozyme hypothesis (which, by the way, someone on WordPress blogged about when it came out) by showing that the catalytic exosome subunit Dis3 has a role in the mitochondria, […]

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