The ABCF proteins in Escherichia coli individually cope with 'hard-to-translate' nascent peptide sequences.

Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.

ATP-Binding Cassette Transporters*/metabolism ; Escherichia coli*/genetics ; Escherichia coli*/metabolism ; Escherichia coli Proteins*/metabolism ; Escherichia coli Proteins*/genetics ; Escherichia coli Proteins*/chemistry ; Peptides*/metabolism ; Peptides*/chemistry ; Peptides*/genetics; Amino Acid Sequence ; Peptide Elongation Factors/genetics ; Peptide Elongation Factors/metabolism ; Protein Biosynthesis ; Ribosomes/metabolism ; Ribosomes/genetics

Organisms possess a wide variety of proteins with diverse amino acid sequences, and their synthesis relies on the ribosome. Empirical observations have led to the misconception that ribosomes are robust protein factories, but in reality, they have several weaknesses. For instance, ribosomes stall during the translation of the proline-rich sequences, but the elongation factor EF-P assists in synthesizing proteins containing the poly-proline sequences. Thus, living organisms have evolved to expand the translation capability of ribosomes through the acquisition of translation elongation factors. In this study, we have revealed that Escherichia coli ATP-Binding Cassette family-F (ABCF) proteins, YheS, YbiT, EttA and Uup, individually cope with various problematic nascent peptide sequences within the exit tunnel. The correspondence between noncanonical translations and ABCFs was YheS for the translational arrest by nascent SecM, YbiT for poly-basic sequence-dependent stalling and poly-acidic sequence-dependent intrinsic ribosome destabilization (IRD), EttA for IRD at the early stage of elongation, and Uup for poly-proline-dependent stalling. Our results suggest that ATP hydrolysis-coupled structural rearrangement and the interdomain linker sequence are pivotal for handling 'hard-to-translate' nascent peptides. Our study highlights a new aspect of ABCF proteins to reduce the potential risks that are encoded within the nascent peptide sequences.
(© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

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JP20H05925 MEXT; Ohsumi Frontier Science Foundation; Japan Foundation for Applied Enzymology; Takeda Science Foundation; Yamada Science Foundation; JST CREST JPMJCR19S2; JST SPRING JPMJSP2108

0 (ATP-Binding Cassette Transporters)
0 (Escherichia coli Proteins)
0 (factor EF-P)
0 (Peptide Elongation Factors)
0 (Peptides)

Date Created: 20240425 Date Completed: 20240609 Latest Revision: 20240611

20250114

PMC11162784

10.1093/nar/gkae309

38661232