Alternative proteoforms and proteoform-dependent assemblies in humans and plants

Variability of proteins at the sequence level creates an enormous potential for proteome complexity. Exploring this complexity is an ongoing goal in biology. Here, we survey human and plant bottom-up native proteomics data for protein truncation variants, where substantial regions of the full-length protein are missing from an observed protein product. In humans, Arabidopsis, and Chlamydomonas, approximately one percent of proteins show a short form, which we can assign by comparison to RNA isoforms as likely deriving from transcript-directed processes or limited proteolysis. While some detected protein fragments align with known splice forms and protein cleavage events, multiple examples are previously undescribed, such as fibrocystin proteolysis and nuclear translocation in a green alga. We find that truncations occur almost entirely between structured protein domains. Intriguingly, multiple protein truncations of phase-separating proteins resemble cleaved proteoforms produced by enteroviruses during infection. Some truncated proteins are observed in humans and plants, suggesting that they date to the last eukaryotic common ancestor. Finally, we describe novel proteoform-specific protein complexes, where loss of a domain may accompany complex formation.