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. 2021 Mar 23;12:1830. doi: 10.1038/s41467-021-21942-6

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© The Author(s) 2021

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 2 — a EF-Tu-derived peptides with one (gray) or two (red) errors in Str-treated wt cells and in untreated ram cells. Shown are means of three technical replicates (n = 3). b Error clusters induced by Str are absent in the ram strain. Str concentration (4 µM) was chosen to achieve the same E_f in wt and ram cells. Peptides with error clusters were detected by QRAS and SRM (rdotp = 1, fragment ions color coded). c Enrichment of error clusters in aggregates. After treating cells with Str (8 µM), EF-Tu was isolated from the soluble cell fraction and the insoluble aggregates and peptides analyzed by DDA. Shown are the means of three technical replicates (n = 3). d Time course (left panel) and concentration dependence (right panel) of Str treatment for D208E-F211L error cluster detected by PRM. Shown are means ± SD of three technical replicates (n = 3). e Str-induced error clusters with three and four substitutions. Target peptides were enriched by QRAS and detected by PRM. f Examples of PRM validation for error clusters in different proteins induced by Str (8 µM). g Types of misreading events in error clusters. Errors with ambiguous classification of the misreading position are shown in gray; in cases where misreading can arise from mismatches at different positions, the errors were classified as originating from the 3^rd > 1^st > 2^nd position mismatch, according to their response to AGA treatment^9–11. h Effect of different AGAs. The error cluster D208E-F211L in EF-Tu detected by PRM upon treatment with spectinomycin (Spc), streptomycin (Str), dihydrostreptomycin (DHS), paromomycin (Par), apramycin (Apr), sisomycin (Sis), gentamycin (Gen), geneticin (G418), hygromycinB (HygB), neomycin (Neo), tobramycin (Tob), kanamycin A (KanA), kanamycin B (KanB), amikacin (Amk), or neamine (Nea) at concentrations that gave rise to maximum misreading (‘Methods’). Shown are means ± SD of three technical replicates (n = 3). See also Supplementary Figs. 1–3 and Source data file.