Table 1_RefSeq-corrected transcriptomic and RNA-interaction integration maps medium-associated vancomycin response rewiring in Staphylococcus aureus.xlsx

Candidate identities were harmonized using USA300HOU RefSeq locus-tag annotations, clean GSE254530 was used for conservative cross-dataset assessment, and published RNase III-CLASH data were used to evaluate candidate-associated RNA-interaction evidence.</p>Results<p>In the exploratory GSE149213 processed-expression contrast analysis, analytically pooled vancomycin-evolved lineages/populations retained broad acute responses, with the strongest response-rewiring burden corresponding to the EVO-WT response shift in RPMI + 10% LB; EVO-MAC response shifts were much more limited.

RefSeq locus-tag harmonization retained a predefined nine-locus candidate panel for evidence ranking. Conservative GSE254530 assessment provided strict cross-dataset differential-expression support for pyrR only, while glnA was uniquely mapped but not differentially expressed and the remaining seven candidates lacked conservative clean-feature mappings. RNase III-CLASH integration highlighted carbamoyl-P synthase, dihydroorotase and glnA as top-ranked candidate-associated CLASH hotspots.

Module-level processed-expression analysis further localized evolved response shifts to RPMI-associated redox/stress, cell-wall/envelope and proteolysis/stress/virulence programs, with translation/ribosome showing a contrasting negative trend.</p>Conclusion<p>This study provides a RefSeq-corrected, evidence-ranked processed-expression map of vancomycin response rewiring in S. aureus. Although the findings remain hypothesis-generating rather than causal, they define prioritized candidate loci, candidate-associated RNA-interaction edges and functional modules for future experimental testing in matched in vitro systems and biologically relevant infection models, including bone- and implant-associated models.</p>