iiinova — where your digital self keeps evolving

Replies

Joanna Masel @joannamasel.bsky.social · 12/12/2024

This suggests that some proteins carried their greater aromatic usage from earlier competing codes to ours. Eg the synthetase domain that distinguishes early amino acids I vs V has a whopping 4.1% tryptophan, with conserved W, I, and V. Distinguishing amino acids predates how we do it now. 12/15

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Joanna Masel @joannamasel.bsky.social · 12/12/2024

Our annotations of LUCA’s domains agree well with recent annotation of LUCA’s full-length genes by @emoody.bsky.social @phil-donoghue.bsky.social. doi.org/10.1038/s415... Recent gene-tree species-tree reconciliation methods are what made inferring LUCA possible for both groups. 13/15

Table showing that 95 of our pre-LUCA Pfams where deemed by Moody et al. to be >75% likely to be in LUCA proteins, 3 were 50-75% likely, 2 were <50% likely, and 1 was not in their dataset. For our single-copy LUCA Pfams, 672 were confirmed at the >75% level, 75 at the 50-75% level, 106 were <50%, and 15 were not in their dataset.

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Eric Fauman (he/him) @ericfauman.bsky.social · 12/12/2024

Can you use the list of domains to say anything about the order of appearance of cofactors? NAD, FAD, SAM, heme, etc.

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ERR_Moody @emoody.bsky.social · 12/12/2024

Awesome stuff!

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Joanna Masel @joannamasel.bsky.social · 12/12/2024

We had previously found an exceptionally long-term trend: older animal domains have their hydrophobic amino acids more interspersed along the primary sequence elifesciences.org/articles/57347, driven by differential loss rates. We confirmed that this trend goes all the way back to LUCA. 14/15

Schematic of hydrophobic residue clustering vs interspersion, and violin plot showing that LUCA domains have more interspersion than post-LUCA, which have more than modern domains. All are more interspersed than the clustering score of 1 expected by chance.

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