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Project no.4

Metabolic evolution

Heterotrophic organisms that rely on obtaining energy through the ingestion of large particles tend to be unable to synthesize a number of key nutrients. Presumably this is because they can readily obtain those nutrients from their prey, relaxing selection to retain the genes necessary for biosynthesis of those key molecules. In humans such nutrients are known as "essential amino acids", and "vitamins". We can't make them, we have to get them from food. This phenomenon is widespread. Many heterotrophic organisms are auxotrophic for a number of key nutrients. Autotrophic organisms, like plants, tend to be able to synthesize the full complement of amino acids and many vitamins, or are generally auxotrophic for a smaller number of complex nutrients. Other organisms that do not eat by ingesting large particles and rather import organic and inorganic building blocks through rigid cell walls, like fungi, are also prototrophic (able to synthesize the complex molecules they need from basic components). 

In this project we ask: What were the metabolic capabilities of the ancestors of today's prototrophs (like plants and fungi)? Focusing on plants and their relatives, presumably the ancestors of plants were single-celled phago-heterotrophs, ingesting other organisms for energy and nutrients. Were those ancestral cells also prototrophs? Were they auxotrophs like today's phago-heterotrophs? How can we tell? We approach this problem by looking for lineage specific patterns of lateral gene transfer to give us clues towards which biosynthetic pathways were supplemented by the endosymbiont genome. 

The Archaeplastida polytomy

The presumed phago-heterotrophic ancestor of most extant photosynthetic eukaryotes entered a symbiotic relationship with a cynaobacterium. Then the lineages diversified into the three recognized primary plastid bearing groups today. The relationship between them is unresolved, but maybe LGTs can give us clues.

Model of endosymbiont gene transfer supplementing a missing metabolic pathway.
LGT patterns in individual pathways and lineages
Lineages cluster based on LGT patterns
One phylogenetic tree showing a split in Archaeplastidan LGTs
All metabolism hairball with two well known pathways highlighted
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