Review of “Tomorrow’s Table” in PLoS Biology

Pamela Ronald and Raoul Adamchak are the husband-and-wife authors of a new book, “Tomorrow’s Table:  Organic Farming, Genetics, and the Future of Food”.  The book is reviewed by Tony Trewavas in PLoS Biology, and sounds like an interesting read.  The review is also good.  Some excerpts from Trewavas’ review:

“The subject matter deals with organic farming methods, GE methods, questions of environmental conservation, risk, trust, and ownership of seeds and genes. The last chapter, and the only one written jointly, concludes that some marriage of organic and GE technology will represent the agriculture of the future.

I must admit to holding the same view some 15 years ago, but not now. I assumed that the use of GE technology would be rather like the green revolution. Universities and research institutes would make new crop plants available and free to those that needed them. What has intervened of course for GE is the input of commercialism, which has muddied the waters. Organic farming is not immune to commercial pressures either, and there are strong suspicions that the organic industry’s antagonism to GE is a marketing ploy. Mutated crops, induced by radiation, for example, have been used for many years by conventional and organic farmers alike, and it is now known that radiation mutation causes much greater genomic change than GE technology [2].”

The bolding in the preceding is mine; the phrase makes a point that I have been convinced of for years.

“The continuing conversation did not resolve the issues between them. It convinced me, however (if I needed convincing), that while everyone is entitled to their opinions, when dealing with detailed technical matters of science or medicine or any subject that requires enormous qualifications and experience, the notion that all opinions have equal validity is simply downright wrong. If you want real information on the safety of heart surgery procedures, do you follow the advice of a qualified heart surgeon or the local butcher? If you want advice on flying a jumbo jet, do you ask the local bus driver or a pilot with 10,000 hours of experience flying jumbo jets? And if you want advice on how to captain a supertanker, do you ask a person whose experience is limited to rowing a dinghy? Mistakes by surgeons are not uncommon, 70% of air crashes result from pilot error, and occasionally supertankers hit the rocks. But relying on rank amateurs instead of professionals would guarantee instant catastrophe. Many branches of science are very complex. However, being a scientist isn’t enough, of course, as being a scientist doesn’t qualify you to advise on any subject except your specialty. To provide advice that can lead to sensible policy requires not only a thorough understanding of the workings and literature of the particular scientific area but many decades of experience in that field.”

The parallels with the ev/ID-cre debate, where all manner of uninformed antievolutionists believe their erroneous opinions are entitled to equal “treatment”, are striking in this passage.

“Although Ronald and Adamchak mention no-till agriculture only briefly, this is surely the agriculture of the future. No-till farms produce only one third of the greenhouse gas emissions of an organic farm [5]. No-till eliminates soil erosion and improves environment, wildlife, and soil. Most importantly, it maintains a conventional yield. Currently 10% of United States farms are totally no-till, and another 60% are partially no-till; this achievement is due almost solely to the availability of GE herbicide-tolerant crops.

No-till is not an amalgam of organic and GE technology but something that was derived from observations of nature in a very different way. Faulkner, the perceptive founder of no-till in 1943 [6], derived his revolutionary ideas from asking himself a very simple question: Why don’t the prairies suffer from the present (1940s) problems of US agriculture? Faulkner’s answer: the prairies are not subjected to that most damaging of all soil treatments: the plough. Leaving crop residues on the surface is the nearest any form of agriculture comes to mimicking the annual and natural cycle of the meadow. Herbicides are human “allelopathy” of weeds, and humans are part of nature too. If you want an agriculture that is nearest nature, then this is surely it.”

This last excerpt is a plug for a practice (no-till farming) that has been pioneered and championed by researchers at the University of Kentucky (among other places); indeed, there is an annual No-Till award and seminar (The S. H. Phillips No-Tillage Seminar) given in my department every fall.

The nuclease aisle

One of the themes that keeps popping up here is that of nucleases.  I thought I would post an adaptation of a table from a recent review by Ciarán Condon that lists the various ribonucleases in E. coli and B. subtilis.  The point is to illustrate the variety of nucleases that exist in bacteria, and to get readers to think more of the importance of RNA processing and, moreso, RNA turnover.

This table is adapted from Condon C (2007), Maturation and degradation of RNA in bacteria, Current Opinion in Microbiology 10: 271–278.  Enjoy.

Spartacus!

Readers of this blog (all two of ya) have met my younger daughter.  The other (Heather) is a senior geology major at the College of Wooster.  She’s also a die-hard band geek (she marched in high school, and is a member of the College of Wooster Scot Band). One of our traditional family summer activities is one or more Drum Corps International shows.  This summer, we got to see the finals in Bloomington IN (a short 3 hour hop, skip, and jump* from Lexington).  Needless to say, this was an excellent show.  From start to finish, the crowd was contagious.  But the crowd’s reaction to the champions’ show was above and beyond.  The new champions are the Phantom Regiment; their show theme was the movie Spartacus.  There is a point where the corps gets to re-enact the “I am Spartacus” scene; the crowd was so charged that, at that point, many, many in the audience shouted out as well.  For fans, the experience was positively electrifying.

DCI will have their championships in Indianapolis for the next several years.  I expect you know where I may be found around the 2nd weekend of August for the foreseeable future.

* 3 hr car trips are going to seem real short by the end of the summer.  Heather is 5 hrs away, and I get to move her stuff up to Wooster this Friday.  Amy will be attending Juniata College, a nifty 9 hrs or so by car (and at least that long a plane trip -one of those “you can’t get there from here” situations).

Polyadenylation, histone mRNAs, and the evolution of irreducible complexity

As if on cue, a new study reinforces some ideas I discussed in another essay.  This report from Joan Steitz’ lab shows that both CPSF73 and CPSF100 contribute important residues for the endonuclease responsible for maturation of histone mRNAs*.  The abstract:

“In eukaryotes, the process of messenger RNA 3′-end formation involves endonucleolytic cleavage of the transcript followed by synthesis of the poly(A) tail. The complex machinery involved in this maturation process contains two proteins of the metallo-beta-lactamase (MBL) superfamily, the 73 and 100 kDa subunits of the cleavage and polyadenylation specificity factor (CPSF). By using an in vitro system to assess point mutations in these two mammalian proteins, we found that conserved residues from the MBL motifs of both polypeptides are required for assembly of the endonuclease activity that cleaves histone pre-mRNAs. This indicates that CPSF73 and CPSF100 act together in the process of maturation of eukaryotic pre-messenger RNAs, similar to other members of the MBL family, RNases Z and J, which function as homodimers.”

The functional and evolutionary implications are fascinating.  Of particular note are the possible roles that gene duplication may have played in the origins of the eukaryotic polyadenylation complex (recall that CPSF73 and CPSF100 are themselves related at the sequence level, and are both metallo-beta-lactamase family members), and the functional similarities with bacterial metallo-beta-lactamase nucleases.  It is also interesting to see how a shared core (CPSF) has assumed different functions, through interactions with different “accessory factors”.  (The notion that U7 and CstF are “accessory factors” is a bit unconventional, to be sure.)  And of course, in keeping with one theme of this blog, the implications that this emerging story has for the origins and evolution of irreducibly complex systems are considerable.

The citation:

Kolev NG, Yario TA, Benson E, Steitz JA. Conserved motifs in both CPSF73 and CPSF100 are required to assemble the active endonuclease for histone mRNA 3′-end maturation. EMBO Rep. 2008 Aug 8. [Epub ahead of print] doi:10.1038/embor.2008.146

*  astute readers may recall that cell-cycle-regulated histone mRNAs are not polyadenylated.  Instead, they have distinctive structures at their 3’ ends, which are formed by a complex that includes the snRNP U7.  It turns out that many of the additional proteins that act in concert with U7 are identical to subunits of the polyadenylation complex.  CPSF73 and CPSF100 are two of these; the scaffolding protein symplekin is another.

Giardia lamblia, polyadenylation, and irreducible complexity

Several of the introductory essays in this blog have dealt with aspects of polyadenylation and the complex that mediates this process.  As shown in this figure and as discussed (in part) here and here, the complex is sizeable and possesses a number of activities, including some that seem superfluous.  However, genetic studies in yeast indicate that virtually every subunit of the core complex is essential – for viability and for pre-mRNA processing and polyadenylation in vitro and in vivo.  Biochemical and/or immunological depletion studies reveal a similar scenario in mammals, and a less-expansive set of studies suggests that a similar rule of thumb will apply in plants.  The bottom line of all of this is that almost all of the subunits of the polyadenylation complex seem to be essential.  In the vernacular of a proponent of intelligent design, the polyadenylation complex would seem to be irreducibly complex.

It is in this context that the recently-completed genome of the parasitic organism Giardia lamblia enters the fray.  Last year, the complete sequence of G. lamblia, some 12 million base pairs, was determined and analyzed.  The authors of the study published in Science noted a number of interesting things – a preponderance of genes encoding protein kinases, evidence for substantial horizontal gene flow from bacteria and archaebacteria, and a streamlined core gene expression machinery (transcription and RNA processing).  This streamlining is especially notable in the case of the polyadenylation machinery.  Remarkably, of all the subunits pictured in this figure, genes for only three* can be found in G. lamblia (see the figure that follows this paragraph).

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.