Fool’s Gold Inside Us, Microbes, and Jumping Genes: Fe-S Cluster Assembly in Oxymonads and Related Protists

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Structure of a [2Fe-2S] cluster (Upper) and [4Fe-4S] cluster (Lower). Frazzon & Dean 2001, 10.1073/pnas.011579098

The mineral pyrite, iron sulfide gemstone also known as fool’s gold for its gold-like appearance, used to be a favorite material for alchemists in their futile struggles to create precious metals. Since antiquity it is also combined with silver in the so-called marcasite jewelry, popular especially in the 19th century, and until today pyrite is used for production of sulfur dioxide for various industrial applications. Whether you are alchemist, Victorian lady, chemical engineer, or anybody else for that matter, you always have a bit of pyrite with you, or rather inside you. The iron-sulfur (FeS) clusters are molecules composed of iron and sulfur atoms arranged in a pattern resembling pyrite crystal structure, which function as cofactors – small molecular “plug-ins” – in a vital group of proteins involved in such important tasks as electron transfer or DNA repair. FeS clusters are found in all living cells and are indispensable for life as we know it. Their ubiquity and importance even led to formulation of a hypothesis saying that pyrite and similar minerals played a crucial role in the very origin of life.

In eukaryotic cells – building blocks of animals, plants, fungi, and microbial protists – FeS clusters are typically produced by two different metabolic pathways. One set of enzymes (ISC) works in mitochondria. The other (CIA), localized in cytoplasm, provides FeS clusters to all the other parts of the cell including the nucleus. The cytoplasmic pathway doesn’t work on its own, but depends on a, yet unidentified, product of the mitochondrial one. Mitochondria are therefore usually essential for the cell and even their most simplified forms tend to have at least this function intact. And so, production of FeS clusters became a central question for our team after we described the first known eukaryote completely devoid of mitochondria, a chinchilla gut-inhabiting protist Monocercomonoides. How can the cytoplasmic pathway build FeS clusters if mitochondria, together with their pathway, were lost? It turns out the answer is lateral gene transfer – sharing of genetic material between unrelated organisms. The ancestors of Monocercomonoides gained another pathway for FeS cluster synthesis, called SUF, from bacteria and recruited it for work instead of the lost mitochondrial one.

Evolution and diversity of Preaxostyla.

Evolution and diversity of Preaxostyla. LVF Novák.

We investigated the evolutionary history of this gene transfer. When did it happen? What other organisms share it? And how did the bacterial SUF pathway change in its new home? We sampled a broad diversity of Monocercomonoides’ relatives constituting a group called Preaxostyla. All of them are single-celled microbes which shun oxygen just like Monocercomonoides, but that’s where the similarity ends. For example, Streblomastix resembles a bundle of snuggly packed symbiotic bacteria, only held together by a network of thin lobes – the actual protist cell. Another one, Saccinobaculus, looks like a bag with a snake inside, which constantly wriggles around. The “snake” is in fact a structure of cellular skeleton that helps the cell to move. Preaxostyla are wonderfully weird creatures indeed! We sequenced 10 species, chosen to cover all major lineages, and found the genes for the SUF pathway in each of them, even those species which, unlike Monocercomonoides, still retain mitochondria. Also, none of the organisms harbored the mitochondrial ISC pathway.

Inventory of SUF proteins in Preaxostyla. Vacek et al. 2018, 10.1093/molbev/msy168

Inventory of SUF proteins in Preaxostyla. Vacek et al. 2018, 10.1093/molbev/msy168

All the 5 genes constituting the SUF pathway in Preaxostyla show the same evolutionary history. That means they must have come in one gene transfer event from bacteria, which happened before all the species split – more than 100 million years in the past. This happened before the mitochondrion vanished, possibly representing the final nail in its coffin. When the mitochondrial pathway was replaced with a new substitute, the microbes simply lost any remaining motivation for keeping the costly organelle and got rid of it. We also found out that 3 of the 5 genes are fused together in Preaxostyla, likely producing a large chimeric protein, a situation not observed in bacteria.

Phylogenetic analysis of concatenated SufB, C, D, and S proteins. Vacek et al. 2018, 10.1093/molbev/msy168

Phylogenetic analysis of concatenated SufB, C, D, and S proteins. Vacek et al. 2018, 10.1093/molbev/msy168

Our findings are most interesting from the evolutionary point of view. They show another strong evidence of lateral gene transfer having a dramatic effect on eukaryotes, a notion which is still controversial. However, they might also have a broader impact in the future. The interesting fusion of 3 genes may indicate that the protein products of these particular genes may be closely cooperating, providing a hint on the general functioning of the SUF pathway. Also, remember that still mysterious connection between mitochondrial and cytoplasmic pathways for FeS cluster production in most eukaryotes including humans? Well, now we have a system where both pathways are in cytoplasm and no mitochondrion is involved. Cross-examination of these different arrangements might help us finally identify the elusive link. Maybe one day, microscopic inhabitants of animal guts will help us uncover the secrets of the gems inside us.

Paper: Vacek V, Novák LVF, Treitli SC, Táborský P, Čepička I, Kolísko M, Keeling PJ, Hampl V: Fe-S Cluster Assembly in Oxymonads and Related Protists. Molecular Biology and Evolution 2018, msy168.

ICOP 2017 in Prague: Getting Around

This summer we are organizing the 15th International Congress of Protistology in Prague, Czech Republic. For more information please visit the congress web page, join the Facebook event, or follow the International Society of Protistologists and particularly the #ICOP17 hashtag on Twitter. Here I made two simple maps which might help you to plan your stay in Prague. For official information on public transport in Prague as well as for finding a particular connection you can use the public transport company page. Please, feel free to contact me with any (nonofficial =) ) questions about Prague or the congress.

map

Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes

Background

Multiple prokaryotic lineages use the arginine deiminase (ADI) pathway for anaerobic energy production by arginine degradation. The distribution of this pathway among eukaryotes has been thought to be very limited, with only two specialized groups living in low oxygen environments (Parabasalia and Diplomonadida) known to possess the complete set of all three enzymes. We have performed an extensive survey of available sequence data in order to map the distribution of these enzymes among eukaryotes and to reconstruct their phylogenies.

Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes

Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes. Graphical Abstract.

Result

We have found genes for the complete pathway in almost all examined representatives of Metamonada, the anaerobic protist group that includes parabasalids and diplomonads. Phylogenetic analyses indicate the presence of the complete pathway in the last common ancestor of metamonads and heterologous transformation experiments suggest its cytosolic localization in the metamonad ancestor. Outside Metamonada, the complete pathway occurs rarely, nevertheless, it was found in representatives of most major eukaryotic clades.

Conclusions

Phylogenetic relationships of complete pathways are consistent with the presence of the Archaea-derived ADI pathway in the last common ancestor of all eukaryotes, although other evolutionary scenarios remain possible. The presence of the incomplete set of enzymes is relatively common among eukaryotes and it may be related to the fact that these enzymes are involved in other cellular processes, such as the ornithine-urea cycle. Single protein phylogenies suggest that the evolutionary history of all three enzymes has been shaped by frequent gene losses and horizontal transfers, which may sometimes be connected with their diverse roles in cellular metabolism.

Continue reading (open access) here.