Alternative proteoforms and proteoform-dependent assemblies in humans and plants

Abstract

Variability of proteins at the sequence level creates an enormous potential for proteome complexity. Exploring the depths and limits of this complexity is an ongoing goal in biology. Here, we systematically survey human and plant high-throughput 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 the green alga Chlamydomonas, approximately one percent of observed proteins show a short form, which we can assign by comparison to RNA isoforms as either 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 our observation of fibrocystin proteolysis and nuclear translocation in a green alga. We find that truncations occur almost entirely between structured protein domains, even when short forms are derived from transcript variants. Intriguingly, multiple endogenous protein truncations of phase-separating translational proteins resemble cleaved proteoforms produced by enteroviruses during infection. Some truncated proteins are also observed in both 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.

The Integration of Data from Different Long-Read Sequencing Platforms Enhances Proteoform Characterization in Arabidopsis

“…The ability to produce multiple proteoforms from a single gene represents an efficient tool for diversifying proteins functions and has an impact over plant physiology, including development and stress response [ 38 , 39 ]. Exploring the depth, significance, and potential of this ability to increase proteome complexity is a main ongoing goal in biology.…”

Quantitative Aspects of the Human Cell Proteome

“…However, this method has mass limitations due to the capabilities of the instruments, and quantification is technically challenging-only relative quantification of proteins can be performed [20]. As the average mass of a human protein is ∼60 kDa, alternate methods are necessary to identify and quantify all proteoforms at high throughput [21].…”