Fig. 4: The roles of P11 stem-loops in C. elegans attraction and nitrogen assimilation. | Nature Communications

Fig. 4: The roles of P11 stem-loops in C. elegans attraction and nitrogen assimilation.

From: Pseudomonas aeruginosa modulates both Caenorhabditis elegans attraction and pathogenesis by regulating nitrogen assimilation

Fig. 4

a Diagram showing putative P11 secondary structure. Yellow: NasT binding site (P11mut1) deletion; purple: rho-independent terminator (P11mut2) deletion; blue: 5’ nucleotide; red: 3’ nucleotide followed by …UUUUUUGUUU, poly-U sequence following the rho-independent terminator. Structure created in RNAfold and visually optimized in rnacanvas.app52. b Model showing the effects of P11mut1 and P11mut2 on nitrogen assimilation operon expression. P11mut1 prevents NasT binding to P11 and transcriptional anti-termination through the leader sequence (top). P11mut1 prevents transcriptional termination and therefore, causes constitutive expression of the nitrogen assimilation operon (bottom). c Relative expression of P11 and nirB in PA14 P11mut1/2 to PA14 WT. Normalized to 5S expression. Dotted line represents limit of detection. p = <0.0001. d Choice assays between PA14 WT and p11mut1/2. CI = (# on PA14 WT PA14 P11 mutants)/(Total). Right-hand CI = (# on PA14 P11mut1–PA14 P11mut2)/(Total) represents last box and whicker plot. e Choice assays between PA14 P11mut1 and nitrogen assimilation/partner-switching gene mutants. CI = (# on PA14 P11mut1–PA14 gene mutant)/(Total). f Choice assays between PA14 P11mut2 and nitrogen assimilation/partner-switching gene mutants. CI = (# on PA14 P11mut2–PA14 gene mutant)/(Total). g Ammonia production of P11 mutants. Colorimetric fluorescence intensity normalized to CFU and multiplied by 105. p = 0.0025. Box Plots: center line = median, box range 25th–75th percentile, minimum/maximum denoted by whiskers, individual choice assay plates are represented by dots and are technical replicates (10 plates/technical replicates for d–f). Bar graph error bars denote SD, center denotes mean, and each dot represents a biological replicate (3 total). One-Way ANOVA, (c–f), Tukey’s multiple comparison test, (g) Dunett’s multiple comparison test using WT as control. *p ≤ 0.05, **p ≤ 0.01, ***p ≤ 0.001, ****p ≤ 0.0001, ns = not significant (Prism 9). For exact sample size (n), all biological replicates, and p values see source data file.

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