The largely unexplored biology of small proteins in pro‐ and eukaryotes

Abstract

The large abundance of small open reading frames (smORFs) in prokaryotic and eukaryotic genomes and the plethora of smORF-encoded small proteins became only apparent with the constant advancements in bioinformatics, genomic, proteomic and biochemical tools.Small proteins are typically defined as proteins of less than 50 amino acids in prokaryotes and of less than 100 amino acids in eukaryotes and their importance for cell physiology and cellular adaptation is only beginning to emerge. In contrast to antimicrobial peptides, which are secreted by prokaryotic and eukaryotic cells for combatting pathogens and competitors, small proteins act within the producing cell mainly by stabilizing protein assemblies and by modifying the activity of larger proteins. Production of small proteins is frequently linked to stress conditions or environmental changes and therefore cells seem to use small proteins as intracellular modifiers for adjusting cell metabolism to different intra-and extracellular cues. However, the size of small proteins imposes a major challenge for the cellular machinery required for protein folding and intracellular trafficking and recent data indicate that small proteins can engage distinct trafficking pathways. In the current review, we describe the diversity of small proteins in prokaryotes and eukaryotes, highlight distinct and common features and illustrate how they are handled by the protein trafficking machineries in prokaryotic and eukaryotic cells. Finally, we also discuss future topics of research on this fascinating but largely unexplored group of proteins.

Bottom‐up and top‐down proteomic approaches for the identification, characterization, and quantification of the low molecular weight proteome with focus on short open reading frame‐encoded peptides

“…Meanwhile, the functions of some SEPs in, for example, cell division, membrane transport, embryonic development, or cell death have been elucidated. Different biological functions of SEPs have been reviewed [12,15,93,94].…”

mRNA targeting eliminates the need for the signal recognition particle during membrane protein insertion in bacteria

“…However, a recent study has demonstrated that under stress conditions, the hyper-phosphorylated guanine nucleotides ppGpp and pppGpp bind to the GTPase domains of both SRP and FtsY and prevent the formation of a functional targeting complex 91 . This is intriguing, because many small membrane proteins, such as YohP, are upregulated when cells encounter stress conditions [107][108][109][110] , but the simultaneous (p)ppGpp accumulation would prevent their membrane insertion by the SRP-pathway 96 . mRNA targeting and SRP-independent protein insertion, as shown here for YohP, could provide a solution to this conundrum and allow for the insertion of stress-response proteins even when the SRP pathway is impaired (Fig.…”

A small protein, derived from an alternative 53BP1 promoter transcript and expressed via translational reinitiation on an internal overlapping ORF, modulates proteasome activity

“…Both these events can respond to intracellular stresses 77–79 . Curiously, it has already been proposed that SEP expression may be an integral part of the cellular “stress response” 80 . The link to developmental functions is also intriguing, because promoter switching and translational reprogramming are key events during differentiation in metazoans 81, 82 .…”