Journal article: Comparative kinomics of the malaria pathogen and its relatives

Hot off the presses!
Structural and evolutionary divergence of eukaryotic protein kinases in Apicomplexa

It's a thorough paper, so I'll cover the highlights here.

Why we study apicomplexans

Apicomplexans are a group of related single-celled organisms which are exclusively parasitic. The best-known member is Plasmodium falciparum, which causes the most virulent form of malaria. Another well-studied species is Toxoplasma gondii, which primarily lives in cats but can infect most mammals.

It's a hugely diverse group. But overall, we know very little about them.

Our main motivation for studying apicomplexan proteins is to find what features make them distinct from human proteins, so we can then design drugs to target those features specifically -- the drug will identify and disable the parasite protein without the risk of affecting the host proteins, too. We study protein kinases, in particular, because a number of drugs have already been designed to inhibit kinases in cancer. The same or similar compounds could be used to treat parasitic diseases, potentially.



From an evolutionary biologist's perspective, apicomplexans are also interesting to study because they belong to an evolutionary branch that is quite divergent from the animals, plants and fungi more familiar to us. By learning about apicomplexan biology, and comparing to other model organisms, we can learn more about eukaryotic diversity and the origin of eukaryotes.

Another perspective on the tree of life

Many people, including scientists, think of evolution as a ladder, with single-celled organisms at the bottom and humans at the top. Different lineages, like green plants and fungi, each branch off the ladder at some intermediate point, but evolution is nonetheless mistakenly thought of as a directed progression from bacteria to protists to fish to humans.

That's wrong. It leads to mistakes, such as considering all protists (single-celled eukaryotes) to be closely related to each other. But even within Apicomplexa, the evolutionary distance between Plasmodium falciparum and Toxoplasma gondii is as great as the distance between humans and mosquitoes.

I'm particularly proud of Figure 1 in the paper, which includes a species tree that inverts the traditional view: The closest human relative, yeast, is at the bottom, and layers of increasingly strange and unfamiliar protists build up to the Plasmodium genus.

Interesting features of proteins and genomes

When apicomplexan parasites invade a host, they secrete a mixture of dozens of different proteins into a protective vacuole formed from the host cell membrane. We'd expect that some of these proteins are essential for invasion and virulence, and therefore good targets for inhibition or diagnosis.

Two apicomplexan-specific protein kinase families are known to be exported. The FIKK family appears in 1 copy in most apicomplexans, but is amplified to 21 copies in P. falciparum and 6 copies in P. reichenowi, and does not appear in any species outside the Apicomplexa. Another family, called rhoptry kinases (ROPK) after the apicomplexan organelle they're localized to, appears in dozens of copies in coccidians (T. gondii, Neospora caninum, Eimeria tenella, Sarcocystis neurona), but not in any other lineage of Apicomplexa. Plasmodium and others still contain rhoptries, but there are no kinases in the protein cocktail those rhoptries contain.

As obligate parasites, apicomplexans evolve under different evolutionary contraints than free-living organisms like yeast and humans. Many genes are no longer necessary, and some may even be a liability if they interact with the host's own biochemical pathways. Because of this, we see widespread gene loss and overall compaction of apicomplexan genomes.

One especially curious case is the loss of upstream regulators of the MAPK cascade -- a signaling pathway found in almost all eukaryotes, consisting of 3 or 4 protein kinases each activating the next in a sort of biochemical relay. Apicomplexans contain 2 to 3 copies of the downstream protein kinase, MAPK, but the rest of the pathway components (STE7, STE11, STE20) are generally lost, and none of the surveyed apicomplexans had a complete MAPK cascade. So there's an open question: What other proteins take the place of the STEs in this important pathway, or have MAPK-like features? Is there an Achilles heel to be discovered?

The project

We:

1. Identified and classified the full set of protein kinases in each of the 17 apicomplexan proteomes available
2. Devised a pipeline to identify apicomplexan-specific ortholog groups in known protein kinase families
3. Compared these ortholog groups to the typical members of the kinase family to find specific sequence motifs that distinguish the divergent ortholog group
4. Mapped these motifs onto protein structures; reviewed the literature to understand possible functions and functional differences related to these motifs

Read about what we found here.