Circular Permutation Obscures Universality of a Ribosomal Protein
Functions, origins, and evolution of the translation system are best understood in the context of unambiguous and phylogenetically based taxonomy and nomenclature. Here, we map ribosomal proteins onto the tree of life and provide a nomenclature for ribosomal proteins that is consistent with phylogenetic relationships. We have increased the accuracy of homology relationships among ribosomal proteins, providing a more informative picture of their lineages. We demonstrate that bL33 (bacteria) and eL42 (archaea/eukarya) are homologs with common ancestry and acute similarities in sequence and structure. Their similarities were previously obscured by circular permutation. The most likely mechanism of permutation between bL33 and eL42 is duplication followed by fusion and deletion of both the first and last β-hairpins. bL33 and eL42 are composed of zinc ribbon protein folds, one of the most common zinc finger fold-groups of, and most frequently observed in translation-related domains. Bacterial-specific ribosomal protein bL33 and archaeal/eukaryotic-specific ribosomal protein eL42 are now both assigned the name of uL33, indicating a universal ribosomal protein. We provide a phylogenetic naming scheme for all ribosomal proteins that is based on phylogenetic relationships to be used as a tool for studying the systemics, evolution, and origins of the ribosome.
KeywordsProtein evolution Zinc ribbon Zinc finger Ribosome Tree of life Translation
Peptidyl transferase center
Pairing adjusted sequence entropy
- E. coli
- T. Thermophilus
- H. marismortui
- P. furiosus
- S. cerevisiae
- T. thermophila
- D. melanogaster
- H. sapiens
- P. falciparum
- T. brucei
The authors would like to thank Dr. Hyman Hartman and Dr. Nenad Ban for discussions. The authors declare that they have no competing interests. This work was supported by National Aeronautics and Space Administration (Grant Numbers NNX16AJ28G and NNX16AJ29G) and NSF Grant 1713995.
NAK, PIP, ASP, and LDW conceived the study. NAK, PIP, and AV collected and analyzed the data. NAK and PIP generated all the figures and tables. NAK, PIP, ASP, and LDW wrote the manuscript.
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