By: Theo Sanderson and Ellen Bushell
Profiling the effects of large-scale gene knock-outs reveals different evolutionary forces acting on different parts of the malaria parasite. Credit: Bushell, Gomes, Sanderson et al. (2017).
How does the malaria parasite work? Better answering that question will assist with developing drugs that destroy the parasite, and potentially with the design of vaccines. The PlasmoGEM project is working to shed light on the parasite’s biology by characterising the role of many of the five thousand genes that make up its genome.
One way to study what a gene does is to “knock it out”, deleting its DNA sequence, and to see whether anything changes in the parasite. Historically this has been a laborious process in malaria parasites, and so until now only a small proportion of parasite genes have been studied this way. We have been working to develop new technologies to speed up the process of knocking out parasite genes and measuring the resulting biological effect.
With these new technologies, we have now been able to test the majority of the parasite’s core genes, and this provides us with the first overall picture of the functionality of the malaria genome, which has been published today.
A general theme of many historic discoveries in malaria biology has been that the parasite often has several ways of carrying out crucial functions. This could make developing drugs against malaria difficult if when one pathway was blocked by a drug, the parasite was simply able to use another. In addition, there are genes which are only involved in certain parts of the parasite’s complex lifecycle. For example some genes are needed only to carry it through the mosquito; others allow it to grow in the liver of the host.
We did all of our experiments in a single stage of the lifecycle - the period in the bloodstream that causes the symptoms of malaria, and so we expected that most genes we deleted would have no effect - either because they were needed in different stages, or because alternative pathways could compensate for their loss. But what we found was a surprise. Two-thirds of the parasite genes we deleted either killed the parasite outright or significantly decreased its rate of growth.
This is a higher proportion of “essential” genes than has been observed in any other organism studied. It may be connected with the fact that as the parasite’s ancestor, which looked something like an algae, evolved to become a parasite it drastically slimmed down its genome, shedding 6,000 genes. This may have been because living inside a host provided a more consistent environment than it had previously experienced in the outside world. This drastic genomic reduction seems to have left the parasite heavily dependent on most of its remaining genes, even at just a single stage of its lifecycle.
In our data we still see the redundant pathways that have long been known in malaria genetics, but these seem to be mostly limited to areas of close interaction between the host and the parasite, where evolutionary arms races lead to diversity and redundancy. In contrast, the remainder of the genes the parasite uses in the blood-stage appear extremely important for growth.
This is an exciting discovery not just as a quirk of evolutionary biology, but because it has important implications for drug development. Any of these essential proteins, if it could be targeted by a drug, would be expected to kill the parasite and cure a patient. The fact that there are many such genes provides a piece of hope amid a background of growing drug resistance.
The data for all of the genes we studied is now available in an online database to allow researchers to prioritise different parasite metabolic pathways for drug development. We hope that this resource advances the fight against malaria, by allowing researchers to quickly find out whether a gene they are interested in represents a redundant component that the parasite can do without, or if it plays a crucial role in allowing the bloodstream growth that causes the symptoms of malaria.
About the authors:
Dr Theo Sanderson is a Postdoctoral Fellow at the Wellcome Trust Sanger Institute, working in Dr Julian Rayner’s group, Human-parasite interactions in malaria, to create new genetic methodologies that allow malaria parasites to be functionally studied at large scale. His experimental work focuses on the mechanism by which the parasite invades the human red blood cell, and he additionally develops novel bioinformatic methods to analyse data from the PlasmoGEM project.
Dr Ellen Bushell is a Senior Staff Scientist at the Wellcome Trust Sanger Institute working in the Rodent Models of Malaria group of Dr Oliver Billker, whose work centers around generating scalable genetic tools and developing screens to functionally analyse the malaria parasite genome at scale. She is the project manager for the PlasmoGEM project.
Ellen Bushell, Ana Rita Gomes, Theo Sanderson, et al. (2017) Functional profiling of a Plasmodium genome shows a high incidence of essential genes in an intracellular parasite. Cell. DOI: 10.1016/j.cell.2017.06.030