Waller Lab for Eukaryotic Diversity and Evolution

Past, present and future research interests

An understanding of eukaryotic evolution can only truly be approached if one takes in the full view of eukaryotic diversity. Protists represent the vast majority of eukaryotic diversity, and hence this is where my attention is drawn. I am interested in the major transitions that have occurred in eukaryotic evolution, and the ways in which cells have responded to these transitions. Particularly, organelle acquisition and remodelling have been strong themes in my research to date, and genome surveys of lesser studied protists have served as important springboards for these studies.

Protists fulfil many essential roles in the environment, ranging from nutrient recycling at a local level, to balancing global carbon cycles with major roles, for marine protists particularly, in carbon fixation and sequestration. However protists are also of outstanding human significance due to their roles as human parasites. My research has targeted several such protist parasites, including apicomplexans Plasmodium falciparum (malarial agent) and Toxoplasma gondii, the trypanosomatid Leishmania spp. and microsporidian Encephalitozoon cuniculi. Thus research in the Waller Lab contributes both to broadening our understanding of eukaryotic diversity and evolution, and to developing insights into parasitic organisms in order to better develop chemotherapeutic strategies for disease treatment and prevention.

Protein import systems in endosymbiotic organelles: plastids and mitochondria

All eukaryotes are the products of at least one merger between a host cell and a prokaryote that lead to the endosymbiotic organelle the mitochondrion. Some of these cells have undergone further endosymbiotic events leading to plastids: either through a further prokaryotic endosymbiosis or eukaryotic endosymbioses where a plastid-containing eukaryote itself becomes an endosymbiont. Thus, eukaryotic evolution has been profoundly shaped by the process of endosymbiosis. Part of the success of these mergers can be attributed to the relocation of most (and occasionally all) symbiont genetic material to the host cell nucleus, enabling centralized control of the organelle, but also requiring the protein products of these genes to be targeted back to the organelle. My research has addressed several aspects of protein targeting to endosymbiotic organelles.

Plastids: My research was the first to identify the two-step targeting system to the malarial plastid in apicomplexans (termed apicoplast) whereby proteins transit first through the ER, before entering the plastid (Waller et al, PNAS, 1998; Waller et al, EMBO J., 2000). Characterization of the bipartite peptide signals that direct this routing enabled the prediction from genomic data of numerous organelle pathways retained by these non-photosynthetic plastids that now offer promising candidates for novel drug targets (Waller et al, Antimicrob. Agents Chemoth. 2003; Ralph et al, Nature Rev. Micro. 2004). The sister Phylum to Apicomplexa are the dinoflagellate algae, and I have also investigated protein trafficking routes to these photosynthetic plastids. Most interestingly, an additional trafficking signal, a stop-transfer membrane anchor, is a conspicuous feature of most although not all dinoflagellate plastid-trafficking signals (Patron et al, J. Mol. Biol., 2005). Thus dinoflagellates appear to employ an alternative route (and possibly multiple routes) through the ER to deliver proteins to their plastids. My group is currently developing transformation technologies for dinoflagellates to enable these trafficking events and signals to be dissected in greater detail. I have also examined the impact of plastid replacement events (a process possibly unique to dinoflagellates) on plastid-protein targeting. This research as uncovered the most profound changes to plastid targeting known for any plastid-containing eukaryote (Patron et al, J. Mol. Biol., 2006; Patron and Waller, BioEssays, 2007).

Mitochondria: I have been involved in the analysis of several components of the yeast mitochondrial import machinery (TOMs and TIMs) through collaborative work with Trevor Lithgow (Bio21, University of Melbourne) (Gentle, et al, J. Cell Biol., 2004; Likić et al, J. Mol. Biol., 2005; Chan et al., J. Mol. Biol., 2006). Using these studies of yeast as a springboard, my group has now undertaken the examination of the mitochondrial protein import apparatus of a most interesting system. Microsporidia are highly specialized obligate-endoparasites derived from fungi and of significance to human health. Severe reductive evolution in response to their parasitic lifestyle has eliminated from the mitochondrion major energy metabolism, the relict mitochondrial genome, and apparently ~90% of the typical mitochondrial proteome. Thus protein import into this near-ghost of a mitochondrial is minimal and the import apparatus has apparently responded accordingly with a heavily stripped down and derived TOM/TIM assemblage remaining. Our research is now dissecting the functions of the relict import proteins that constitute this skeletal import apparatus, and novel features of this system may offer scope for drug design against this pathogen for which little effective chemotherapy exist.

Mitochondrial genome organization in dinoflagellates

Organelle genomes in dinoflagellates show a true penchant for oddity. Dinoflagellate plastid genomes were first described as uniquely deviant from other plastids, where multiple mini-circles encoding 1-3 genes occur in place of a single multi-gene circular chromosome. We have now tacked the subject of the mitochondrial genome in dinoflagellates, and have uncovered equal novelty (Jackson et al, BMC Biol., 2007). We have shown that, common with apicomplexans, the dinoflagellate mitochondrial genome is gene-poor, encoding only three proteins and two heavily fragmented rRNA subunits. However, unlike in Apicomplexa, each gene occurs multiple times in many different genomic contexts (up to 10 times at least for one gene). Moreover, many genes are fragmented, and we show that at least one is reconstituted through mRNA trans-splicing. Most bizarre of all, at least two of the protein genes are transcribed without any potential termination codon. Currently we are investigating mitochondrial translation termination to address how such a fundamental process has been altered. We are also addressing the chromosomal arrangement in dinoflagellate mitochondria as it remains unknown whether there are single or multiple, linear or circular chromosomes.

Genome evolution through endosymbiotic and lateral gene transfer

As genomic data for a broad range of eukaryotes has become available, there has been a fascinating revelation of the role of transferred genes in eukaryotic evolution. Genes can transfer laterally between distinct, free-living taxa (lateral gene transfer, LGT), or between genomes within endosymbiotic partnerships such as plastids and mitochondria (endosymbiont gene transfer, EGT). My research has identified some more unusual but biologically very significant LGT processes by analysis of genomic and/or cDNA data and molecular phylogenetics. These include prokaryote to eukaryote transfer of operons that result in protein fusions in their eukaryote destinations (Waller et al., Mol. Bio. Evol., 2006), and transfer of functional gene clusters responsible for toxic secondary metabolite synthesis in fungi (Patron et al., BMC Evol. Biol., 2007).

Endosymbiont gene transfer (EGT) from plastid and mitochondrial endosymbionts to the host nucleus, is a process that has been accepted for several decades however analysis of more recent endosymbiotic events allows us a fresh understanding of this process and its significance. The dinoflagellate Karlodinium micrum has recently replaced its ancestral plastid with a new one (by engulfment of another photosynthetic algae, a haptophyte). We have shown that EGT has again been an important process in centralizing the genes for this new plastid into the host nucleus. However, analysis of numerous genes for plastid proteins reveals that many ancestral plastid-protein genes remain, and now service the new plastid (Patron et al., J. Mol. Biol. 2006). Thus plastid acquisition, in this case, was only partially accompanied by EGT, and re-targeting of old plastid proteins has created a plastid with a chimeric proteome. EGT from plastids and mitochondria has also been argued to contribute more broadly to cell metabolism in non-organelle functions, however the full extent of this has been difficult to measure due to the antiquity of primary endosymbiontic events. The dinoflagellate, K. micrum, offers an excellent opportunity to quantify the genetic contribution that this recent eukaryotic endosymbiont has made to non-plastid functions, and this is a current research program in my laboratory.

Structure-function analysis of common cellular features shared amongst diverse eukaryotes

Three disparate Phyla, the dinoflagellates, apicomplexans and ciliates, have been firmly united as sister groups by molecular phylogenies despite substantial differences in cell structure and lifestyle. One conspicuous cellular feature, however, has been identified as common to all groups, a system of flattened membrane sacs (known as the inner membrane complex, alveoli or amphiesma) immediately beneath the plasma membrane. This feature has given rise to the informal classification of the three in Infrakingdom Alveolata, yet little common organization or function of this feature has been described across this assemblage. We have identified proteins that are known to be associate with the inner membrane complex (IMC) in apicomplexans, as being present in both dinoflagellates and ciliates as well, providing the first biochemical feature uniting them. We have shown that these proteins are associated with the IMC in all groups, and provide an opportunity to dissect the common biogenesis and architecture of IMCs throughout Alveolata. Analysis of such common features is fundamental to understanding the evolution and divergence of eukaryotes.

Research projects in the lab

To help explore these fascinating biological questions, I'm always looking for people to join our lab. We use a broad mixture of: molecular biological techniques (including genomic and EST gene surveys, and gene phylogenies); cell biological techniques (including fluorescence and electron microscopy, green fluorescent protein-tagging in live cells, and antibody localisation studies); and functional complementation experiments.

If you're interested in joining us contact Ross to discuss current projects and opportunities in the lab.

If you're just happy to surf our website, might I suggest browsing the following links:

Pictures tell a thousand words, they also reveal our weakness for powerful microscopes and things that glow in the dark

Publications also tell a thousand words. Some are even longer!

People in the lab will often tell a thousand words if you give them a chance

Protists − who are they, are they important, and who studies them