The polyadenylation complex – Endonucleases

Messenger RNA 3’ end formation involves an RNA processing step.  It is thus natural to assume that the polyadenylation complex (as illustrated here) includes at least one subunit that is an endonuclease (an enzyme that cuts the RNA within the polynucleotide chain, as opposed to at the 5′ or 3′ ends).  Indeed, the complex does include such a nuclease.  However, just as there seem to be more RNA binding proteins than known cis element, there may be a multiplicity of endonucleases in the complex.  Specifically, at least two CPSF subunits (CPSF73 and CPSF30) have been shown to possess endonucleolytic activity in vitro (1-4).  The research community would probably consider that CPSF73 is the most probable candidate for THE processing endonuclease, but the possibility that CPSF30 serves this role, along with or instead of CPSF73, cannot be ruled out.  (Except perhaps in yeast, whose CPSF30 counterpart, Yth1, apparently lacks the nuclease activity seen in other eukaryotic homologs [5].)

Alternative polyadenylation

Polyadenylation is a process that pertains to the expression of almost all genes in eukaryotes.  In addition, as is the case with virtually every step in the process, polyadenylation is a step at which regulation may occur.  The most obvious way by which this might occur is via what is commonly known as alternative polyadenylation.  Alternative polyadenylation, in a nutshell, involves the use of alternative poly(A) sites within a single gene.  The general idea is shown in Figure 1 – any gene that has more than one poly(A) site has the potential to be processed at any of the various sites.

One person’s junk is another’s treasure

In previous essays (here and here), we learned that genes encoding new proteins can and do, often, arise de novo in the course of evolution, contradicting one of the central tenets of ID proponents.  The means by which these genes arise are many.  One of these, suggested by Cai at al. (the subject of one of the earlier essays), involved the adaptation of a gene encoding an evolutionarily-conserved non-coding RNA via the appearance, by mutation, of appropriate translation initiation and termination (“start” and “stop”) codons.  This mechanism represents an intersection of sorts between the subject of protein evolution and another matter of discussion on these blogs, namely the existence, evolution, and “function” of junk DNA.  In this essay, I review a 2007 study by Debrah Thompson and Roy Parker (“Cytoplasmic decay of intergenic transcripts in Saccharomyces cerevisiae”, Mol. Cell. Biol. 27, 92-101) that adds a great deal of clarity to this mode of gene and protein evolution.

Junk to the Second Power

(Introductory remark – this is another repost of a Panda’s Thumb essay, included on this blog as a segue of sorts for the essay that follows this one. As always, enjoy…)

The ID blogosphere is much agog, and has been for some time, about recent (and not so recent) results that suggest some sort of functionality in what has long considered to be nonfunctional (junk) DNA in eukaryotes. The most recent buzz centers on studies (such as ENCODE ) that indicate that large swaths of so-called junk DNA are “expressed” by RNA polymerase II. Apparently, the fact that RNA polymerase transcribes alleged junk DNA is a blow to Darwinism, and a feather in the cap of ID. Their excitement in this regard, I suspect, will wane greatly once they learn some of the true implications of these results. For the matter of “expression” in junk DNA is one wherein ID meets, and gets swallowed by, the Garbage Disposal.

What follows is a discussion of a relatively recent report that rains on the ID parade. As is my habit, I’ll summarize the essay for those with short attention spans – the bottom line is that the so-called “function” that so excites the ID proponents may be little more than manifestations of quality control in gene expression, and that the supposed functional swaths of non-coding junk DNA may be nothing more than parts of the genome that encode, and lead to the production of, “junk” RNA (if I may so bold as to coin a phrase). In a nutshell, junk piled on top of junk.

The polyadenylation complex – RNA binding proteins

As I indicated in the overview of polyadenylation, this process is mediated by a complex of proteins called, naturally enough, the polyadenylation apparatus. This machinery has been reviewed many times over the years, and the review I pointed to earlier provides a nice overview of the subunits involved. An illustration from this review is below the fold at the end of the essay; this illustration and the review will serve as the source for much of this information, and will take the place of what would be a long list of citations that pertain to the details that follow. Rather than re-invent the wheel, what I thought I would do is to summarize things taking a different approach. Thus, what I will try to do in the next few essays is to discuss things from the perspective of the biochemical activities one finds associated with the complex, with special attention being paid to unexpected or unexplained aspects of the complex. As well as being a list, I hope that these essays will raise in readers’ minds one or two questions about the process, questions likely without answers at the moment.

The 2008 Plant Molecular Biology Gordon Conference

Next week (July 13-18), I’ll be attending the Plant Molecular Biology Gordon Conference in Holderness, NH.  Given the policy of the Gordon Conferences (everything that happens at a GRC, stays at a GRC), I won’t be providing any “blow-by-blow” account of the meeting.  However, I thought readers might be interested in the agenda.  This gives one a good idea as to what is “hot” at the moment, and where the field will be moving in the next few years.  The following may also be perused at the meeting web site.  I’ve only listed the talks and speakers – no need to dwell on the, um, social aspects of the meeting.

Regulatory evolution, agriculture, and RNA – a possibly interesting intersection

Much of the interest and excitement in the field of “Evo-Devo” today centers on the roles that changes in gene regulation may play in the evolution.  This mechanism (altering when and/or where a particular gene is expressed during development) stands apart from that concerning changes in the actual structure and function of individual proteins.  A recent study from Steve Tanksley’s lab brings this phenomenon into focus for this blog, and may tie together some different themes.

This study (Cong et al., Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication, Nature Genetics 40, 800-804, 2008 ) deals with one of the two processes (cell cycle control and organ number determination) associated with the enlargement of tomato fruit size in the course of domestication of this crop.  Many years of QTL mapping have led researchers to regions of the tomato genome involved in these processes.  The study by Cong et al. describes the end result of the characterization of one of these QTLs, a locus that is a major contributor to organ number (specifically, carpel number).

Addenda for my reply to Kirk Durston

Over at Recursivity, I left a comment in response to some things Kirk Durston said about my analysis of a paper by Doug Axe.  Blogspot doesn’t like my formatting, so I have moved the last few paragraphs here, and posted the link to this message on Jeffrey Shallit’s blog.

The last two paragraphs:

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4.  The occurrence of functional islands in sequence space is far less rare than you let on, Kirk.  The scope of the problem for you is illustrated (briefly, and among other places – I apologize for the shameless self-promotion) here, here, and here.

5. Said occurrence may be far more common than you let on, Kirk.  Studies such as those of Chiarabelli et al. (Chemistry and Biodiversity 3, 840-859, 2006) show  that folded sequences are rather common (20%!) in collections of random polypeptides.  This is a large part of the problem of function, and it’s not nearly the impossibly inaccessible one you imply.

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Here is the rest of the comment, in case anyone is wondering about what the fuss is about: