There’s a highly emotional, not merely scientific, controversy raging about function. The ENCODE project announced that 80% of the human genome is functional, but as Jonathan Wells noted earlier, a group at Oxford University now claims only 8.2% is. Nature reports on the controversy without taking sides, but states that the dispute turns upon the way one defines function.

ENCODE assumed that if something is transcribed, it is functional. The Oxford group assumes something is functional if natural selection has conserved it. However, there’s a more natural, intuitive definition: see what the gene or protein actually does. If it does some work that keeps the cell alive and healthy, that’s a function. Taking that approach, geneticists and biochemists are continuing to find processes that are actually — or at least potentially — functional, often in the "junkyard" of misunderstood phenomena. Here are some recent examples.

Amino-acyl tRNA Synthetases

What does a "catalytic null" sound like? Probably, a do-nothing enzyme; a freeloader. A paper in Science, though, describes an international team that found "Human tRNA synthetase catalytic nulls with diverse functions."

The tRNA synthetase family (AARS) is a vital group of enzymes that attach the appropriate amino acid to a transfer RNA (tRNA) based on its triplet codon. The AARS family is, therefore, the key to the genetic code, matching the genetic language of codons to the protein language of amino acids.

When the synthetases are assembled by the spliceosome, some are left with their primary catalytic domain missing. This leaves some "catalytic nulls" (CNs) floating around like headless chickens. But do they flop around, just getting in the way? No, the researchers found:

Here we report discovery of a large number of natural catalytic nulls (CNs) for each human AARS. Splicing events retain noncatalytic domains while ablating the catalytic domain to create CNs with diverse functions. Each synthetase is converted into several new signaling proteins with biological activities "orthogonal" to that of the catalytic parent. We suggest that splice variants with nonenzymatic functions may be more general, as evidenced by recent findings of other catalytically inactive splice-variant enzymes. (Emphasis added.)

Far from being junk, these "catalytic nulls" are important signaling molecules, not only for the AARS family, but for many other enzymes. Intuitively, a signal implies an important function: letting two parties know how to respond to a change in status. This understanding converts much of the junkyard into essential gear!

The authors point out that the number of CNs seems to increase as one goes up the Tree of Life: "Genetic efficiency in higher organisms depends on mechanisms to create multiple functions from single genes." In their view, evolution was the mechanism, the creator. It hit on new functions in a random fashion as the spliceosome churned out variants. "As the Tree of Life is ascended, 13 new domains, which have no obvious association with aminoacylation or editing, have collectively been added to AARSs and maintained over the course of evolution, with no appreciable benefit or detriment to primary function," they say. Presumably, the cell, like a tinkerer in a workshop, found something useful for the new accidental CNs to do. "The paradox of strongly conserved noncatalytic domains progressively added to AARSs protein structure over the course of evolution appears to be at least in part an evolutionary reshaping of tRNA synthetases for other functions," they say.

That interpretation is not required by the data, however. It is just as reasonable to assume that each higher organism has the CNs it needs to thrive. How would a mindless process relying on chance "reshape" anything, anyway, "for other functions"?

Some of these new domains are appended to each of several synthetases, whereas others are specific to a single synthetase. Notably, these novel domain additions are accretive and progressive; and while their persistence provides no major benefit to aminoacylation, the strong evolutionary pressure for their retention suggests they are not random functionless stochastic fusions, but may be conserved for a specific biological purpose, perhaps distinct from the canonical enzymatic function.

Pick your origin story as you please; the point is, what was previously thought to be nonfunctional does, in fact, have useful work to do. They give some examples:

Possibly, functional expansion of AARSs was to link translation at the first step of protein synthesis to a variety of cell signaling pathways. Recent studies have demonstrated roles for specific AARSs in pathways associated with angiogenesis, inflammation, the immune response, mammalian target of rapamycin (mTOR) signaling, apoptosis, tumorigenesis, and interferon-? (IFN-?) and p53 signaling. The work detailed here suggests that the universe of AARS-derived entities, which are active for nontranslational functions, may be far greater than anticipated.

The light came on when these researchers were willing to look "orthogonal" to the expected function. It was like thinking outside the box or taking the blinders off. The "Junk DNA" notion, by contrast, leaves the blinders on.

Long Non-coding RNAs

These molecules (lncRNA for short) were snatched from the genetic junk pile in recent years. A paper in PNAS shows that when scientists choose to look for function in the junk pile, they usually find it. This time, ENCODE motivated their quest:

The role of noncoding RNAs in mammalian biology is of great interest, especially since the Encyclopedia of DNA Elements [ENCODE] results were published. We and others have studied microRNAs in the heart, but little is known about their larger cousins, long noncoding RNAs (lncRNAs). Here, we used genome-wide sequencing and improved bioinformatics to quantify lncRNA expression in mouse hearts, define a subset of cardiac-specific lncRNAs, and measure dynamic lncRNA regulation during the transition between embryo and adult, and in the adult heart after experimental pressure overload (a model resembling human hypertensive cardiomyopathy). We linked specific regulated lncRNAs to cardiac-expressed mRNAs that they target and, through network analyses, discovered a broader role of regulated cardiac lncRNAs as modulators of key cardiac transcriptional pathways.

This sheds light on why the human genome codes for so few proteins. As they found, "The vast majority of mammalian DNA does not encode for proteins but instead is transcribed into noncoding (nc)RNAs having diverse regulatory functions."

Notice how these findings support the definition of function as having a vital job to do. We’re not just seeing if the piece of DNA is transcribed; we’re not seeing if evolution conserved it. We’re looking at what it actually does.

Small Interfering RNAs

The name sounds like the quintessence of anti-function. They’re small, and they interfere. What are these "small interfering RNAs (siRNAs)" there for? They are another example of presumed cellular debris that turns out to be vital, so much so that figuring out what they do is "exciting" to researchers: In Current Biology, Julie M. Claycomb of the University of Toronto reports, "Ancient Endo-siRNA Pathways Reveal New Tricks."

Enabled by the advent of high throughput sequencing, there has been an explosion in the identification of endo-siRNAs in all three kingdoms of life since the discovery of the first microRNA in 1993. Concurrently, our knowledge of the variety of cellular processes in which small RNA pathways related to RNA interference (RNAi) play key regulatory roles has also expanded dramatically. Building on the strong foundation of RNAi established over the past fifteen years, this review uses a historical context to highlight exciting recent developments in endo-siRNA pathways.

You can read the paper for specifics, but you get the point: another class of junk is "exciting" researchers with newly found "key regulatory roles" — i.e., functions.

The Nucleolus

This example is about an "obscure organelle" known as the nucleolus. Science describes the growing respect for a cellular player long thought to have only one job:

For more than 30 years, researchers thought that the nucleolus performed a vital but circumscribed role in the nucleus — manufacturing a specific type of RNA, dubbed rRNA, that assembles into ribosomes, the organelles that make proteins. But scientists have come to realize that, as molecular cell biologist Robert Tsai of the Texas A&M Health Science Center in Houston puts it, "the nucleolus is much more complex than rRNA synthesis."

Besides serving as a ribosome factory, the organelle also functions as a command center that monitors a cell’s condition and orchestrates responses when it’s under stress. By storing certain proteins and doling them out when they are required, the nucleolus "endows cells with an accurate way to regulate distribution of proteins," says Michal Hetman, a molecular and cellular neurobiologist at the University of Louisville in Kentucky. Ultimately, the nucleolus helps determine whether cells reproduce and when they die.

The nucleolus is so important that cancer researchers are seriously evaluating it as potential target for intervention. The "plurifunctional nucleolus" is its new moniker. "The nucleolus has turned out to be a busy cellular housekeeper."

Researchers Expecting to Find Function Appear to Be on a Roll

Don’t they? Well, it’s more exciting to look for function than for junk, and it’s more satisfying when you find it.

Grumpy Darwinists like Dan Graur are setting themselves up for a fall when they insist that the genome is full of leftover junk from a blind, aimless past. When that Oxford paper came out, Nature says he exclaimed, "What an amazing birthday present." He commented, "It is ‘idiotic’ to suggest that a part of the genome could be functional if it didn’t respond to pressure from natural selection."

Someone should remind Graur of the proverb, "Keep your words sweet. You might have to eat them."

Photo credit: David, Bergin, Emmett and Elliott/Flickr.