Census II: cross-species census of ribosomal protein N-termini — supplementary data, source data and code

This data and reproducibility archive supports the manuscript “An rRNA-embedded ribosomal protein N-terminus loses its methionine: a cross-species census, a genome-scale test and a local-compatibility hypothesis for assembly” (Yie-Hwa Chang, 2026; bioRxiv preprint, submitted to Nucleic Acids Research). Methionine aminopeptidases remove the initiator methionine when residue 2 is small and uncharged, and loss of this activity is lethal in bacteria and yeast. The archive asks whether the structural environment of a ribosomal protein N-terminus predicts its processing class across lineages, whether the same association holds in sequences without structure, and whether the constrained termini are already in place while the subunit assembles. The census comprises 68 ribosome structures from 61 species, 1,873 family × species records and 95 ribosomal protein families, 58 of which switch processing class between species. Termini embedded in rRNA without protein contact were predicted to retain methionine in 18% of records, against 45% of protein-contacted and 41% of solvent-exposed termini. Eight additional structures from separate species corroborated this pattern, which was attenuated under joint family-by-domain stratification. Processing labels are sequence-based predictions from residue 2, validated against 393 directly observed termini from 12 species (98.7% agreement). Thirty-one families never switch class in any sampled species (25 permissive, 6 methionine-retaining), and eleven of the permissive families are threaded into rRNA. The genome-scale layer contains 942,984 family × genome records from 21,485 UniProt reference proteomes, collapsed from 1,027,359 sequences of 94 families. In 6,924 out-of-sample bacterial reference proteomes, exploratory clade-block permutation tests supported an order-level residue-2 association that is sensitive to taxonomic rank and multiplicity: it survives Holm adjustment across the ten bacterial tests (p = 0.036 and 0.019) but not across the thirty tests of the three domains analyzed separately (0.117 and 0.057). The archaeal and eukaryotic tests are coverage-limited (six and eight eligible families) and inconclusive. In yeast assembly intermediates, the conserved uS12 and eS27 termini already occupy their mature environments. The findings indicate a conserved association between rRNA embedding and methionine removal and suggest that local compatibility of processed termini with rRNA contributes to it; they do not demonstrate an assembly requirement, and the census is offered as a resource for testing this hypothesis at named termini. The record contains Supplementary Tables 1–3 (the 393 observed termini; the nine 40S termini of Nagai et al. placed in the census; the 31 class-conserved families), Supplementary Data 1–5 (the census and holdout structures; coordinate reconstruction and revision analyses; the domain-mechanism, four-family and Spraguea proteomics audits; the 40S assembly extension with its structural sources; and the genome-scale sequence layer with the corrected clade-block and separate-domain analyses), the source-data workbook underlying Figures 1, 2, 4 and 5 and Supplementary Figures 1–5, the formatted four-family evidence workbook, the census, statistics and figure scripts as run, an environment specification, and SHA-256 hashes for every file. A re-retrieved structural source archive supplies the coordinate, SIFTS, validation, and UniProt inputs of the four-family audit; 298 of its 379 files are byte-identical to the frozen 22 September 2026 inputs, four entries received a wwPDB minor revision on 23 September 2026 affecting only an administrative date field, and the SIFTS mappings are the current release, as documented in the per-file verification table inside the archive. The Spraguea proteomics source extracts (PRIDE PXD044467) are referenced by URL and hash rather than redistributed. Structural observations are not independent biological replicates. Predicted processing classes are not measurements of terminal state, deposited assembly intermediates do not establish an ordered maturation pathway, and the genome-scale inference is exploratory. See README.md and RESULTS_SUMMARY.md in Supplementary_Data_5_Genome_scale.zip for the multiplicity and coverage limits, and the superseded-analysis notes inside the scripts archive. Companion record for the first (human) census: Zenodo DOI 10.5281/zenodo.22966146 (concept DOI 10.5281/zenodo.22129640); companion preprint “A structural census links penultimate-residue class to N-terminal burial in human protein assemblies”, bioRxiv DOI 10.64898/2026.08.31.748389. A catalog manuscript in preparation uses this release rather than republishing it. Cite this archive as version 1.0.0 using DOI 10.5281/zenodo.22981236. Author-provided analysis software and its documentation are distributed under the MIT License. Author-created datasets, tables, figure source data, and documentation are licensed under Creative Commons Attribution 4.0 International (CC BY 4.0), except where third-party rights apply. Copyright © 2026 Yie-Hwa Chang. Third-party inputs redistributed for reproducibility (wwPDB, PDBe/SIFTS, UniProt, ENA, NCBI, EMDB, PRIDE) retain the terms of their source archives. See LICENSE.txt in the archive.