Friday, 18 December 2015

6th genome of Christmas: the deadly Plasmodium... plant?

If humans have an arch enemy, it might well be the tiny, blood-borne parasite Plasmodium falciparum. This nasty beast causes most of the malaria in sub-Saharan Africa and, together with its cousins, in many tropical zones throughout the world. It kills huge numbers of children every year, and constantly cycles through the bloodstreams of its many survivors. It has been with us since our explosive migration out of east Africa, and in fact many genetic diseases (including sickle-cell aneamia and thalassemias) are tolerated by human populations because they confer an advantage against this nasty parasite.


This intimate, long-standing, dysfunctional relationship makes it all the more weird that Plasmodium falciparum is, in part, ancient, degenerate algae.


Genomics made it possible to untangle this story. As people honed in on the DNA of the Plasmodium parasite, they noticed that the genome was very biased: there were far more A+T than G+C pairings. (The base-pairing rule says there must be the same amount of A+T and G+C because of the double-stranded nature of DNA, but the ratio of A+T to G+C can be different.) This bias caused all sorts of issues, but there was one bit of DNA that looked very different. 

In the 1970s and 80s, people thought this must be the mitochondrial DNA of the parasite. (Mitochondria, the power plants of cells, have their own tiny genome, a remnant of the ancient merging of their ancestors as free-living bacteria with eukaryotic cells. Plasmodium, being a eukaryote, must have mitochondria.) But PCR experiments on classic mitochondrial conserved regions did not turn up anything to support this hypothesis.


In the mid 1990s this "anomalous" part of the Plasmodium genome was cloned by a group from NIMR, the MRC institute in north London now merging to become part of the Crick. A real surprise was that this was not a mitochondrial genome at all - it was a plastid genome, that is to say, the photosynthetic organelle found in all plants and algae (look for the plastid in another Christmas-genome post). The chloroplast was also free-living bacteria before symbiosing with eukaryotes to give rise to plants and algae as we now know them. Furthermore, the whole set of parasites had this degenerate plastid (“apicoplast”), and so were promptly renamed “apicomplexans”.


Quite why a presumably free-living-algae-related organism decided to chuck in a photosynthetic, light-powered life to become one of the world’s deadliest parasites to many species, one can only speculate. 

The apicoplast seems to be important in the parasitic life cycle. One might imagine an organelle specialised for light gathering and carbon fixation might seem pretty superfluous for an endo-parasite (but apparently it's not). This does clear up why a number of anti-malarials, such as Quinine, also act as herbicides; their anti-plastid action hurts both plants and malaria (but of course not all herbicides can be anti-malarial drugs).


Given the importance of Plasmodium, sequencing and assembling the full genome was a priority. However, the traditional step-by-step approach, by which individual pieces of genome were cloned within E. coli, did not work. E. coli spat out the A+T rich DNA most of the time, or (even worse) chopped it up and rearranged it. 

So Bart Barrell and colleagues at the Sanger took to chromosomal sorting and whole-genome shotgun sequencing to sort out the Plasmodium genome - another epic undertaking for its time. With its extreme A+T richness, this genome was a weird beast. You could almost predict coding-sequence regions by eye, as there had to be more G+C to support the amino acids that were clearly present. Furthermore, the ends of chromosomes ('sub-telomeric regions', in the jargon) were freakishly similar, and full of a sophisticated molecular “chaff” (called 'Rifins') that sit on the outside of the parasite as any ever-changing coating, to confuse the host immune system and prevent an effective response from the host.

The community is continuing to sequence other species of Plasmodium, most notably in light of its specialisation to a specific host (i.e., us) - other Plasmodia are less fussy about their host (far broader choice of mammals will do for most parasites), but also less deadly. Furthermore, understanding variation in this parasite, in particular those variations that affect drug resistance, is a monumental, on-going effort at the heart of our struggle to defeat this malicious plant.