Table 1.
How many names is enough for a single protein family?
| Protein name | Representative organism | Gene ID | Name origin | References |
|---|---|---|---|---|
| pY | Thermus thermophilus/Escherichia coli | TTHA0270/yfiA | Because this protein was discovered by Marat Yusupov and colleagues during their studies of Thermus thermophilus ribosomes, it was named “Protein Yusupov” or pY. Later, homologous proteins were found in other bacteria, where they are sometimes referred to as pY. | Yusupov and Spirin (1988) |
| RaiA | Escherichia coli | yfiA | Early studies have established the inhibitory impact of this protein on in vitro protein synthesis. Hence, it was also named “Ribosome associated inhibitor A.” | Agafonov et al. (2001) |
| YfiA | Escherichia coli | yfiA | Some refer to this protein using its gene name, using the uniform nomenclature proposed and developed by Demerec and colleagues. | Agafonov et al. (1999) |
| Long HPF | Escherichia coli | yfiA | Proteins RaiA and HPF from E. coli belong to the same protein family and have a similar structure, except for the C-terminal protein extension in RaiA that is absent in HPF. To distinguish between HPF and RaiA and their homologs in other species, many prefer to use the term “short” and “long” HPF to indicate that the short one is similar to E. coli protein HPF (known to cause the formation of ribosome dimers with protein RMF), as opposed to protein RaiA (that makes ribosomes hibernate in their monomeric state). | Maki and Yoshida (2021) |
| YhbH | Escherichia coli | yhbH/hpf | Named after its gene. | Maki et al. (2000) |
| HPF | Escherichia coli | yhbH/hpf | Due to its ability to bind to ribosomes in metabolically inactive cells and induce formation of ribosome dimers (where HPF acts in cooperation with RMF), this protein was named as Hibernation Promoting Factor. | Polikanov et al. (2012) |
| Short HPF | Escherichia coli | yhbH/hpf | Same origin as the “long HPF.” | Sato et al. (2009) |
| Msmeg_3935 | Mycobacterium smegmatis | Msmeg_3935 | In the dystopian novel “Brave New World” by Aldous Huxley characters are named by numbers instead of names. Similarly, in M. smegmatis studies, proteins are typically identified by their gene names, reflecting their designated number in mycobacterial genomes. For instance, “Msmeg_3935” denotes gene number 3935 in M. smegmatis. | Trauner et al. (2012) |
| Ribosomal protein S30AE | Mycobacterium smegmatis | Msmeg_3935 | Some databases and research articles use the term “ribosomal protein S30AE” to denote this hibernation factor. This naming is based on the structural resemblance of HPF/RaiA and the protein to archaeao-eukaryotic ribosomal protein S30, which likely stems from a shared evolutionary origin between S30 and HPF/RaiA. | Trauner et al. (2012) |
| mpY | Mycobacterium smegmatis | Msmeg_3935 | Using the original name “protein Y,” some studies call the mycobacterial homologs of this protein “mpY” to add some mycobacterial flavor. | Li et al. (2018) |
| RafH | Mycobacterium smegmatis | Msmeg_3935 | One established role of hibernation factors in mycobacteria is to aid their survival under hypoxic conditions by protecting their ribosomes. Therefore, a study proposed to name this protein “ribosome-associated factor under hypoxia” or RafH. | Kumar et al. (2024) |
| Psrp1 | Spinacia oleracea | PSRP1 | Initially, this HPF/RaiA-type protein was mistakenly designated as a plant-specific ribosomal protein 1 (Psrp1). However, it was later discovered to be a chloroplast-specific ribosome hibernation factor. The name, however, is still in use not only for its homologs from chloroplasts in other species but also for those found in bacteria, especially photosynthetic cyanobacteria. | Sharma et al. (2010) |
| LrtA | Arabidopsis thaliana/Cyanobacteria | lrtA | Because the activity of this hibernation factor, belonging to the HPF/RaiA type, is regulated by light in chloroplasts of plants and in cyanobacteria, it was named Light-repressed protein A. | Contreras et al. (2018) |
| Rv0079 | Mycobacterium tuberculosis | Rv0079 | Similarly to Msmeg_3935 from M. smegmatis, HPF/RaiA is named in M. tuberculosis after its gene. | Kumar et al. (2012) |
In the story of the Tower of Babel, God decides to punish arrogant people by inventing new languages to prevent them from understanding each other. It seems that a similar issue exists in the field of ribosome hibernation, where homologs of the same protein have different names in different organisms or even in the same organism (with Mycobacterium smegmatis being the prime example). To help our readers, we have created a catalog of the most common names of proteins from the HPF/RaiA family. We show that this craving for pseudonyms arises from independent discoveries of the same protein in different species or is driven by the fact that some species encode more than one isoform of HPF/RaiA factors, creating a need to discriminate between them.