Furthermore, it highlights some recent developments on protein trafficking of small proteins. The current review focuses on the large variety of small proteins in prokaryotes and eukaryotes and their functional diversity. Equally important are studies on how cells handle folding, targeting, and transport of small proteins, because our current understanding about these processes is almost exclusively based on studies with larger proteins ]. This highlights the importance of functional studies on small proteins in different species. A classification of small proteins based on function ] would be more appropriate, but such a classification is still limited by the small number of detailed functional studies. Furthermore, for differentiating between proteolytic cleavage products and ribosome-generated products, the term micropeptide could be misleading and the term ‘small protein’ is probably a better choice. Although these terms highlight their small size as common denominator, they fall short in describing the enormous functional diversity of small proteins in prokaryotes and eukaryotes. A recent analysis using ribosome profiling, computational analyses, mass spectrometry-based proteomics, and CRISPR- Cas9 knockout studies identified several hundred small proteins in humans, which are important for cell growth by largely unknown mechanisms ].ĭespite their obvious abundance, there is so far no uniform nomenclature for small proteins and many different terms have been used, for example, smORF-encoded polypeptides (SEPs) ], small single transmembrane domain proteins (STMD proteins) ], micropeptides ], miniproteins ], or microproteins ]. The initial algorithms used by genomic studies to identify ORFs worked with a cutoff of 150 nucleotides in prokaryotes and 300 nucleotides in eukaryotes, disregarding translation products of 5000 proteins of < 50 amino acids, most of them uncharacterized. Finally, we also discuss future topics of research on this fascinating but largely unexplored group of proteins.ĭefining the total number of different proteins in a given cell is a major analytical challenge, and several predictions were originally implemented in genome annotation studies for reducing the complexity of these analyses. 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. 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. 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. 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. Small proteins are typically defined as proteins of < 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. 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 bioinformatic, genomic, proteomic, and biochemical tools.
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