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Fig. 2. Acquisition of organelle complexity and function by paralogous gene family expansion. (A) Gene duplication events lead to more than one copy of an open reading frame A (ORF A). This gene redundancy allows each member of the new family to accumulate sequence variation and, hence, potentially new functions. A clear example of this type of event would be the ancestor of the coatomer and adaptin complex subunits. (B) Model for compartment number expansion by gene duplication of protein factors implicated in vesicle identity, specificity and fusion. The progenitor compartment contains, at least, a member of the Rab family, a syntaxin and a coat system (grey). Duplications of the genes encoding these factors facilitate differentiation of function (red, purple), yielding discrete organelles. This process continues in some cases, so that the A1 compartment further is differentiated to A1a and A1b (light and dark blue, respectively), whereas A2 is not elaborated. This may yield a new organelle or differentiation of an organelle into sub-domains or pathways in the case of the coatomers and adaptins (which yielded the cis-Golgi and trans-Golgi network). This general process could eventually have given rise to the organellar complement and machinery reconstructed as present in the LCEA. (C) Paralogous expansion appears variable across the eukaryotes and across machinery; all of the gene families shown were probably present in the LCEA but exhibit different levels of expansion in modern eukaryotes. Specifically there is little evidence for multiple genes encoding tether complex factors in most genomes, while at the other extreme there are many Rab and SNARE genes. Intermediate situations are found for the coatomer, adaptins and syntaxin-binding (SM) proteins; in some lineages either entire complexes or specific subunit families are expanded.
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