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bioRxiv · 10.64898/2026.07.15.738673

Promoter architecture diversifies ParR-dependent transcription in Pseudomonas aeruginosa

Zhu, Z.·Zhao, N.·Song, Y.·Fan, D.·Ying, J.·Nong, C.·Liu, T.·Duan, C.·Zheng, Y.·Zou, S.·Mou, X.·Ma, H.·Liu, H.·Bao, R.
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Abstract

Two-component systems convert environmental signals into transcriptional responses, but how one response-regulator phosphorylation state produces different outputs at different promoters remains unclear. Here we show that promoter architecture determines how the ParR response regulator in Pseudomonas aeruginosa interprets phosphorylation. Phenotypic, transcriptomic, biochemical and promoter-engineering analyses showed that phosphorylation of the conserved ParR receiver residue Asp57 lowered DNA-occupancy thresholds across target promoters. Individual promoters, however, converted this shared increase in binding into activation, repression or phosphorylation-dependent sign switching. Chromosomally D57 ParR variants reproduced these behaviours at endogenous loci and altered antibiotic susceptibility, biofilm formation and virulence-associated phenotypes. Mapping and engineering of representative promoters identified a two-tier cis-regulatory code: half-site sequence compatibility determines productive ParR engagement, whereas spacer length determines regulatory sign and magnitude. Spacer swaps were sufficient to reprogram promoter logic between regulatory modes. These findings separate regulator state from promoter decoding and show how bacterial promoter architecture can diversify the outputs of a shared phosphorylation signal. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/738673v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@1a0a26forg.highwire.dtl.DTLVardef@10836a8org.highwire.dtl.DTLVardef@3c6cd8org.highwire.dtl.DTLVardef@10dfefb_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsParR coordinates antibiotic resistance, biofilm formation and virulence-linked phenotypes in P. aeruginosa. Promoters convert ParR phosphorylation into activation, repression or sign switching. Half-site compatibility and spacer length form a cis-regulatory code for ParR output.

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Zhu, Z., Zhao, N., Song, Y., Fan, D., Ying, J., Nong, C., Liu, T., Duan, C., Zheng, Y., Zou, S., Mou, X., Ma, H., Liu, H., Bao, R.. 2026-07-16. Promoter architecture diversifies ParR-dependent transcription in Pseudomonas aeruginosa. https://doi.org/10.64898/2026.07.15.738673

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