Modulation of Multiple Gene Clusters' Expression by the PAS-LuxR Transcriptional Regulator PteF

Abstract

PAS-LuxR transcriptional regulators are conserved proteins governing polyene antifungal biosynthesis. PteF is the regulator of filipin biosynthesis from Streptomyces avermitilis. Its mutation drastically abates filipin, but also oligomycin production, a macrolide ATP-synthase inhibitor, and delays sporulation; thus, it has been considered a transcriptional activator. Transcriptomic analyses were performed in S. avermitilis DpteF and its parental strain. Both strains were grown in a YEME medium without sucrose, and the samples were taken at exponential and stationary growth phases. A total of 257 genes showed an altered expression in the mutant, most of them at the exponential growth phase. Surprisingly, despite PteF being considered an activator, most of the genes affected showed overexpression, thereby suggesting a negative modulation. The affected genes were related to various metabolic processes, including genetic information processing; DNA, energy, carbohydrate, and lipid metabolism; morphological differentiation; and transcriptional regulation, among others, but were particularly related to secondary metabolite biosynthesis. Notably, 10 secondary metabolite gene clusters out of the 38 encoded by the genome showed altered expression profiles in the mutant, suggesting a regulatory role for PteF that is wider than expected. The transcriptomic results were validated by quantitative reverse-transcription polymerase chain reaction. These findings provide important clues to understanding the intertwined regulatory machinery that modulates antibiotic biosynthesis in Streptomyces.

Keywords: LuxR; PAS domain; Streptomyces; antifungal agent; gene regulation; polyene macrolide.

Figure 1

Growth and antibiotic production in YEME medium without sucrose. Strains S. avermitilis wt (red), and ΔpteF mutant (ochre). (A) Growth curves; (B) Filipin production; (C) Oligomycin production. Arrows indicate RNA samples’ harvesting times.

Figure 2

Differentially expressed genes in the mutant strain ΔpteF. Volcano plots show differential gene expression distribution during exponential phase (A) and stationary phase (B). Statistically significant genes are shown in green (log₁₀ p-value ≥ 1.3).

Figure 3

Transcription profiles of secondary metabolite gene clusters genes in S. avermitilis ΔpteF. Only clusters whose transcription was affected by the mutation are included. All the genes of a given cluster are shown in the plot, including regulatory genes. Colored squares are the plots of differential transcription values for individual genes in the mutant. pte, filipin (red); ave, avermectin (orange); olm, oligomycin (yellow); pk, polyketide (gray); nrp, non-ribosomal peptide (green); ptl, neopentalenoketolactone (purple); geo, geosmin (teal); ezs, albaflavenol/albaflavenone (white); gbl, γ-butyrolactone (dark blue); avs, vibrioferrin-like siderophore (light blue); melC-1, melanin (black).