Significant number of small proteins with less than 50 amino acids remain uncharacterized in different microbial species

Small proteins have attracted
significant research interest recently principally as it was a neglected class
of proteins in the early proteomics era. Usually running far ahead of larger
proteins during gel electrophoresis, small proteins typified by having fewer
than 50 amino acid residues are not commonly analyzed and thus neglected. In
addition, some mass spectrometry methods such as matrix-assisted laser
desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) could not
ionize small proteins efficiently, or their flight time could not be timed
precisely to afford routine detection of such proteins. On the other hand,
while small proteins would theoretically be detected by liquid chromatography
tandem mass spectrometry (LC-MS/MS), short retention time presents challenges
to their facile analytical detection. Hence, the experimental picture of small
proteins cast the light that they could not be efficiently detected and analyzed,
which meant that they may not be well characterised. Such a postulation is
validated by the present work that sought to understand the types of proteins
that constitute small proteins in different microbial species. Results reveal
that significant number of small proteins in different microbial species that
span bacteria, archaea and eukaryotes are not characterised. No function or
name could be annotated for such proteins, which suggests that understanding of
their existence remain at the level of gene sequence profiled by automatic gene
finder during whole-genome sequencing and assembly. This then opens up a vast
vista for the detection, isolation, purification, and analysis of such
uncharacterised proteins. Knowledge of their gene sequence offers the first
step as it opens the way for their heterologous expression in Escherichia
coli, which provides sufficient protein material for isolation,
purification, and characterisation in downstream biochemical assays. Overall,
knowledge of small proteins at the level of biochemical function, and binding
partners remain poor due in large part of their uncharacterised status in
different microbial species. Future work could build on our understanding of
the genetic repertoire of microbial species to proactively express, through
heterologous means, small proteins for biochemical characterisation. Attached
with this preprint is a list of microorganisms with significant number of
uncharacterised small proteins.