Gene Assembly in Ciliates - A glimpse into biological information processing

When researching material for a term paper on biocomputing, I came across a fascinating group of critters called ciliates. Ciliates are unicellular organisms that process their genomic information in a peculiar and unique way, one that was fascinating to study for the computer scientist side of me. In ciliates, we find a very illustrative example of how biological systems use structure as information. Plus they use pointers and linked lists.

 
There they are. Some ciliates. [Image from http://www.liacs.nl/~rbrijder/views_gene_assembly/]

Ciliates, unlike other eukaryotes, have two different kinds of nuclei: macronuclei and micronuclei. A macronucleus is used in the everyday operation of the organism, for synthesizing the proteins it needs to survive. A micronucleus only comes into play during sexual reproduction (I'm stressing this because ciliates can also reproduce asexually). During sexual reproduction, two ciliates recombine their genetic material. The result is somewhat unusual: instead of yielding 2+n organisms - two parents, n children - this reproduction transforms the two original organisms which are then more like twins than anything else.
This is odd to begin with, but the way this works is even more interesting. Because after exchange of genetic material, each of the individuals discards its macronucleus and assembles a new one from the genetic material in the micronuclei.

Now, the genetic material as stored in the micronuclei is highly redundant and scrambled. Parts of genes are scattered all over the micronucleic genome, and during gene assembly, these scattered parts are cut and pasted back together. The mechanism of this, as last I heard, is not entirely understood. But we do know that fragments of genes contain pointers - short DNA sequences at the end of a fragment that match the start of the next fragment somewhere in the micronucleic genome. To me, this looked an awful lot like linked lists, with genes being the entire list and gene fragments being the list elements, chained together by pointers that link the one element to its successor. However, this can't be the whole picture, because the "pointers" in the micronucleic genome are not unique - some pointers are only three bases long and point to any number of locations in the genome. One hypothesis is that the macronucleic DNA is not entirely discarded at first, but serves as a "template" for the genome-in-making. However, this, too, leaves some questions open.

The other point I alluded to earlier - about structure being information - is an important concept in pretty much every type of biological information processing, and it also comes in during gene assembly. The assembly process relies on the three-dimensional structure of the DNA molecules to bring gene fragments together and align them in a way that lends itself to their cutting and pasting. Bazinga.

So much for a brief overview of gene assembly. If you're hooked: There is one book on the subject that gives a good overview, "Computation in Living Cells: Gene Assembly in Ciliates" by Ehrenfeucht et al. Maybe this is your starting point for going down the rabbit hole of biological information processing.

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