Wednesday, October 13, 2010

the gates of immortality?

The Scientist | I had to wonder, what is aging after all? Is it something positively tangible, something that we could define otherwise than a loss: loss of fitness, loss of potential, loss of viability? There is at least one type of molecular marker that correlates well with aging, at least in yeast: extrachromosomal ribosomal DNA circles (ERCs). These circles, or plasmids, of DNA are excised from the ribosomal DNA (rDNA) locus on the chromosome and replicate at each division cycle. The ERCs, however, are redundant to the chromosomal ribosome genes—unnecessary elements that accumulate in the nucleus of the mother cell as it ages. Although ERCs do not represent the only mechanism of aging in yeast, their accumulation is related to aging: cells in which ERC formation is delayed live longer, whereas cells with increased ERC formation die sooner. It would follow then, that their retention by the mother cell contributes largely to the age asymmetry between mother and bud.

Mortal and immortal lineages
Most buds produced by a mother cell will also become bud-producing mothers themselves. A new mother has the capacity to produce 30 buds before she dies with a large number of extrachromosomal rDNA circles (ERCs) accumulated in her nucleus. When the barrier separating the mother from the bud was experimentally disrupted, it allowed ERCs to enter the bud in large number. As a result, the mother lived longer, while the reproductive life of her daughters was shortened proportionate to the amount of ERCs she received.

ERC retention, then, must rely on some intrinsic asymmetry of the nucleus. For example, the yeast nucleus, which does not disassemble during mitosis, as in mammalian cells, always sends its oldest spindle pole body (SPB) to the bud. The SPB, which organizes the duplicate genomes during mitosis, is embedded in the nuclear envelope, and duplicates at each cycle to form a single new SPB. If we forced the nucleus to send the old SPB to the bud only half of the time, would the ERCs then segregate to the bud the other half of the time? To our surprise, this did not happen; the ERCs remained in the mother cell. The exclusive retention of the ERC plasmids within the nucleus of the mother cell only diminished when we disturbed the septin diffusion barrier that divided the nuclear envelope.8

As a consequence, yeast cells lacking the septin diffusion barrier can pass these molecular markers of aging to their daughters. Without the diffusion barrier the mothers were longer lived, but their daughters behaved as if they were older at birth: in other words, they had the capacity to replicate fewer times. The fact that ERCs remained in the mother’s part of the nucleus indicated that the plasmids had to be linked to something embedded in the nuclear membrane. Since septins only blocked diffusion of molecules in the membrane (they did not, for example, create a webbing across the cytoplasm), none of the molecules freely floating in the nucleoplasm would be affected. We observed that these plasmids were associated with the nuclear envelope, more precisely with the basket of nuclear pores on the inside of the nuclear membrane, and that this association was required for their retention in the mother cell. Taken together, our data suggest the intriguing idea that aging, whatever it is, respects diffusion barriers, and that these boundaries prevent the propagation of aging-related molecules into newborn buds.

It may be that the cell’s solution to its unsolvable problems is simply to age, to compartmentalize the components that bear too much resemblance to self and slough them off.

It is still unclear at this point whether these findings have any parallel in other eukaryotes, but we think they might. Indeed, the process of sperm generation shows intriguing similarities with the budding process in yeast, at least in terms of the maturation of the future sperm’s nuclear envelope. The emergence of the sperm head involves the migration of the nucleus through a perinuclear ring. During this process, the nuclear envelope is combed, leaving behind its nuclear pores, which, in many cases, are then excluded from the sperm nucleus. Thus, it is tempting to speculate that we, too—like yeast—keep our sperm as young as possible each time we prepare to form a newborn.

Over the years, these observations and findings have led me back to Gödel and his ideas of unsolvable problems. Aging seemed the perfect example of a process in which the cell could not detect ambiguous molecules (either overtly damaging, or beneficial) and repair itself.

To my mind, ERCs are emblematic of objects that are ambiguous to the cell. They have the same chemical nature, the same repeating composition as the chromosome, and therefore cannot be targeted for destruction without risking damaging the chromosomes as well. They take on the characteristics of entities that are both self and nonself. Gödel was able to mathematically characterize the unsolvable problems he encountered and describe them with a universal rule. Might ERCs help define the universal properties of the unfixable errors that accumulate with age? What prevented biological systems from being complete?

At its core, the generation and accumulation of ERCs is a problem of symmetry—ERCs are generated by errors in DNA repair. When the DNA repair (or recombination) machinery resolves the Holliday Junction, it has one of two options, excision or repair. But because of the local symmetry at the Holliday Junction, the recombination machinery cannot detect a difference between the incoming strands of DNA, and therefore cannot favor one solution over the other. In order to handle such an unsolvable problem, the cell simply produces both outcomes with equal probability, with the production of ERCs and DNA repair occurring exactly 50 percent of the time.

What if structural asymmetries, such as cell polarity, might have actually emerged to counteract the logical problems that symmetric events such as DNA repair generate for the cell? If true, it implies that studying symmetric processes in biology could reveal new insights about aging.

It may be that the cell’s solution to its unsolvable problems is simply to age, to compartmentalize the components that bear too much resemblance to self and slough them off, producing a life that lacks these deformities. Although the yeast cell might not be able to distinguish ERCs from the chromosomes, it found ways to sort them out and confine them to the mother cells. Diffusion barriers could play a central role in this process. It is interesting because they are likely to simply retain in the mother cell anything that is not actively being chosen and pulled into the bud, such as chromosomes or vesicles. Thus, they offer a remarkable solution to the retention of ambiguous objects, that is, objects that the cell cannot distinguish as being right or wrong, objects that therefore remain invisible to cellular machineries.

Last, if aging is a consequence of Gödel’s theorem in biology and of the cell’s incompleteness, then aging is not a program but an inescapable fact. The quest for a cure to the aging “disease” will inevitably fail. But there is a bright side to the fact that the cell is logically incomplete. Would any complete system—one able to detect any damage and repair itself perfectly—have the ability to evolve?