The Small RNA World – a brief introduction

The first reflex when coming across the title of this blog is, most likely, that it is a blog that mentions microRNAs and small RNAs. Up until now, I suppose that I’ve been a disappointment, as the scientific focus has been on the subject matter of my lab – polyadenylation. But this changes with this essay, an overview of the field of small RNAs. My goal with this overview is to lay a foundation to which I can refer in other contexts. As always, enjoy (and feel free to ask questions or correct any mistakes you find).

The 2008 Winners

… of the Albert Lasker Basic Medical Research Award are Victor Ambros, David Baulcombe, and Gary Ruvkun.  These scientists are pioneers in the field of small RNAs, and have helped dissect the process in animals and plants.  Some snippets from The Lasker Foundation announcement:

The 2008 Albert Lasker Award for Basic Medical Research honors three scientists who discovered an unanticipated world of tiny RNAs that regulate gene activity in plants and animals. Victor R. Ambros (University of Massachusetts Medical School, Worcester) and Gary B. Ruvkun (Massachusetts General Hospital, Boston, Harvard Medical School) unearthed the first example of this type of molecule in animals and demonstrated how the RNAs turn off genes whose activities are crucial for development. David C. Baulcombe (University of Cambridge) established that small RNAs silence genes in plants as well, thus catalyzing discoveries of many such RNAs in a wide range of living things. His findings led to the identification of the biochemical machinery that unifies numerous processes by which small RNAs govern gene activity.

Ambros, Baulcombe, and Ruvkun did not set out to unveil small regulatory RNAs. Ambros and Ruvkun were studying how the worm Caenorhabditis elegans develops from a newly hatched larva into an adult. Baulcombe, in a seemingly unrelated line of inquiry, was probing how plants defend themselves against viruses. All three investigators possessed the open mindedness, wisdom, and experimental finesse to entertain the possibility—and then verify—that tiny RNAs could perform momentous feats. Their work has led to the realization that these molecules are pivotal regulators of normal physiology as well as disease.

A few paragraphs later:

Across the Atlantic, David Baulcombe, then of the Sainsbury Laboratory in Norwich, UK, was studying how plants resist viruses. When he and others added to viral-infected plants unusual versions of viral genes, the mRNA copies of the normal genes as well as the newly introduced ones disappeared. Similarly, experimentally added non-viral genes suppressed activity of plant genes that contained similar sequences. Baulcombe proposed that such gene silencing occurs when RNAs embrace target mRNA—through typical Watson-Crick base-pairing—and promote destruction of the mRNA or interfere with its translation into protein. However, no one could find such RNAs.

Baulcombe reasoned that the predicted RNAs might have eluded researchers because the molecules were shorter than anyone imagined and thus, experiments had not been designed to detect them. In 1999, he and a postdoctoral fellow in his laboratory, Andrew Hamilton, devised a hunt specifically for small RNAs. They added test genes to plants and found 25-nt long RNAs that matched; furthermore, these small RNAs appeared only under conditions in which target mRNA activity was shut off. The stunning similarity in size between the plant and worm RNAs suggested that small regulatory RNAs exist in many organisms. Furthermore, it hinted at the presence of cellular machinery that dedicates itself to creating these precisely sized molecules and then uses them to quash gene activity.

Readers are encouraged to read the paper by Hamilton and Baulcombe that started to reveal the true scope of the RNA Underworld.  And another paper from Baulcombe’s group that ties in an underlying theme of this blog to the subject of small RNAs and silencing.  As always, enjoy.

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.

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.

You have to spend money to make money

(Introductory comment – this is a verbatim repost of an essay originally published on The Panda’s Thumb.)

In biology, genetics, biochemistry, and molecular biology classes, one of the things that we used to learn that distinguishes prokaryotes from eukaryotes is the “fact” that eukaryotes have polyadenylated mRNAs, while prokaryotes do not. This morphed rather easily into a distinction – eukaryotes do polyadenylation, prokaryotes do not. For years, this was standard fare in class. However, even as generations of students (beginning with the discovery of polyadenylate tracts in hnRNA in eukaryotes) were learning of this distinction, we knew that all was not right with this. Among the lurking pieces of conflicting data was that the first biochemical entity that was shown to add poly(A) tracts to RNAs in vitro was a bacterial one, isolated and purified from E. coli (1).