Tuesday, July 21, 2009

Interesting Elements #1: Cassandra

This will be the first of hopefully many blogposts where I will focus on one of the more interesting examples of a TE or other parasitic nucleic acid. This will mainly be my outlet to showcase how diverse mobile DNA is and spread the word about weird, interesting or obscure selfish elements which I find in the literature.

Cassandra elements are non-autonomous LTR retrotransposons that were identified in several species of angiosperm plants and ferns (Kalendar et al., 2008). Cassandras are part of of category of non-autonomous LTR elements known as TRIMs (terminal repeat retrotransposon in miniature) which possess the characteristic flanking long terminal repeats (LTRs) on either side of a small core sequence which encodes none of the proteins typically seen in LTR elements (Witte et al., 2001). TRIMs, like Cassandra, are thought to retrotranspose by parasitizing the various proteins of autonomous LTR elements by competing with autonomous transcripts. What makes Cassandra different is that it has a 5S rRNA gene inserted into both of its LTRs.

LTRs contain the regulatory sequences important for transcription of LTR-bearing retroelements, including retroviruses and ERVs, and normally LTR retrotransposons have RNA polymerase II promoters in their LTRs to get the job done. However, Cassandra appears to be using the endogenous RNA polymerase III promoter at the 5' end of the inserted 5S rRNA instead. Analysis of the 5S rRNA sequence also suggested that it might under selective restraint, possibly allowing Cassandra to better bind to transcription factor II proteins to initiate transcription more easily or to take advantage of the paucity of methylation that occurs in normal 5S rRNA promoters, allowing Cassandra to escape suppression by the host genome.

How did the 5S rRNA get there though? The authors hypothesize that long ago ( around 270 million years ago at least based on the phylogenetic distribution of Cassandra) a 5s rRNA-derived SINE (short interspersed nuclear element, a non-autonomous non-LTR retrotransposon) inserted into the LTR of a proto-Cassandra element. This insertion may have conferred a selective advantage on that element, for aforementioned reasons, and allowed it to flourish.

So we have a parasite ( a 5s rRNA-derived SINE) of a parasite ( a non-LTR retrotransposon) inserting into a parasite (TRIM) of another parasite (autonomous LTR retrotransposon) and subsequently being exapted for a new function.

Kalendar, R., J. Tanskanen, W. Chang, K. Antonius, H. Sela, O. Peleg, and A.H. Schulman. 2008. Cassandra retrotransposons carry independently transcribed 5S RNA. Proceedings of the National Academy of Sciences of the United States of America 105: 5833-5838.

Witte, C., Q.H. Le, T. Bureau, and A. Kumar. 2001. Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes. Proceedings of the National Academy of Sciences of the United States of America 98: 13778-13783.

Sunday, July 12, 2009

Selfish DNA: Dawkins

The origins of the selfish DNA hypothesis, later elaborated by Orgel and Crick and Doolittle and Sapienza (1980; both to be covered in a future post), reside in one of the more popular books written by Richard Dawkins The Selfish Gene. For those who haven't read it the book is essentially Dawkins' treatise on how he feels the sole units of evolution are genes and most of everything else is just an extrapolation from this level. Although I disagree with Dawkins' assertion that genes are the fundamental units and targets of selection I do recognize that he was the first to propose that the copious amounts of seemingly superfluous DNA found within metazoan genomes could be explained using his selfish gene theory.
In his own words, from the 30th anniversary edition of the book, pages 44-45:

"Sex is not the only apparent paradox that becomes less puzzling the moment we learn to think in selfish gene terms. For instance, it appears that the amount of DNA in organisms is more than is strictly necessary for building them: a large fraction of the DNA is never translated into protein. From the point of view of the individual this seems paradoxical. If the 'purpose' of DNA is to supervise the building of bodies it is surprising to find a large quantity of DNA which does no such thing. Biologists are racking their brains trying to think what useful task this apparently surplus DNA is doing. From the point of view of the selfish genes themselves, there is no paradox. The true 'purpose' of DNA is to survive, no more and no less. The simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA."

Only a few sentences but they would be the beginning of what was to come next in 1980. More on that in the next post.

P.S. Sorry that this is so short, stay tuned.