Scrambled Genomes

Though less Fungal (and more fungal, if you’ll grant me that) than most of the stories we cover, a recent analysis of the Diplonema papillatum mitochondria genome sequence is interesting nonetheless. The genome consists of over 100 chromosomes, each roughly 6 kilobasepairs (kbp) or 7 kbp in size. However, each chromosome contains only a short (less than 500 bp) gene encoding region. It appears that genes are scrambled, where modular genetic units are dispersed across many chromosomes. Curiously, despite having discontigous genes, cDNA sequencing identifies contiguous and properly ordered mRNA. So just how are scrambled genes expressed and asssembled?

Marande and Burger were able to determine, through an analysis of cox1, that gene modules are individually transcribed, transcripts of the C-terminal containing modules uniquely undergo polyadenylation, and that concatenation of separate module transcripts yields contiguous mRNA. Regarding this last point, it seems that transcript processing is different from distinct from known trans-splicing mechanisms, in such that sequence surrounding the gene modules is nonconserved and display no signatures of known splicing junctions. It would seem some unknown mechanisms sews module transcripts together to generate full length mRNA. The authors suggest that RNA editing may play a role in this gene sewing process, as six nonencoded uridines were found in the cox1 transcript between module boundaries, though guide RNAs involved in any such mechanism have yet to be discovered.

While this genome architecture may be derived and the mRNA assembly process may be complex, it is interesting to think about this system from the standpoint of early genomes. Akin to the ‘introns early’ school of thought, it may be that early DNA encoded gene modules, perhaps on very short chromosomes, that, either randomly or via a mechanism of some sort, were adjoined post-transcriptionally to create fully functional transcript units. Over time successful module permutations could end up co-localizing into autonomous units, resulting in genes as we know them in most systems. Certainly there’s a great deal of speculation here, but it seems that Diplonema papillatum’s mitochondrial genome suggests such a process is feasible.

Leave a Reply