Inactivation of the GacA response regulator in Pseudomonas fluorescens Pf‐5 has far‐reaching transcriptomic consequences

Abstract

The GacS/GacA signal transduction system is a central regulator in Pseudomonas spp., including the biological control strain P. fluorescens Pf-5, in which GacS/GacA controls the production of secondary metabolites and exoenzymes that suppress plant pathogens. A whole genome oligonucleotide microarray was developed for Pf-5 and used to assess the global transcriptomic consequences of a gacA mutation in P. fluorescens Pf-5. In cultures at the transition from exponential to stationary growth phase, GacA significantly influenced transcript levels of 635 genes, representing more than 10% of the 6147 annotated genes in the Pf-5 genome. Transcripts of genes involved in the production of hydrogen cyanide, the antibiotic pyoluteorin and the extracellular protease AprA were at a low level in the gacA mutant, whereas those functioning in siderophore production and other aspects of iron homeostasis were significantly higher in the gacA mutant than in wild-type Pf-5. Notable effects of gacA inactivation were also observed in the transcription of genes encoding components of a type VI secretion system and cytochrome c oxidase subunits. Two novel gene clusters expressed under the control of gacA were identified from transcriptome analysis, and we propose global-regulator-based genome mining as an approach to decipher the secondary metabolome of Pseudomonas spp.

A bacterial symbiont is converted from an inedible producer of beneficial molecules into food by a single mutation in the gacA gene

“…S10). Instead, the edibility difference between the strains must result from some other, unknown downstream effect of gacA, which is not surprising given that its inactivation affects expression of 10% of the genes in the genome (32).…”

“…fluorescens, the GacA-GacS system is a global regulator for antibiotic production (31,32). Upon binding to an as-yet-unidentified external signal, this regulatory system upregulates the production of pyrrolnitrin, and downregulates the production of siderophores such as pyochelin.…”

RNA pentaloop structures as effective targets of regulators belonging to the RsmA/CsrA protein family

“…1,22,25,26,30 The pltA gene is part of an operon specifying pyoluteorin biosynthetic genes. 31 The expression of the secondary metabolite pyoluteorin is under strong positive control of the Gac/Rsm system in P. fluorescens. [31][32][33] Here, we show that the pltA pentaloop (AGGGA) is an effective RsmA/ 12 and the RsmE repression factor was 3.2 (Table 1; pME9524).…”

“…31 The expression of the secondary metabolite pyoluteorin is under strong positive control of the Gac/Rsm system in P. fluorescens. [31][32][33] Here, we show that the pltA pentaloop (AGGGA) is an effective RsmA/ 12 and the RsmE repression factor was 3.2 (Table 1; pME9524). As found previously, the empty vector plasmid pME6001 had an unexplained negative influence on lacZ expression (Fig.…”

“…31,32 The phlA gene is the first gene of an operon specifying DAPG biosynthesis. 34 An RsmA/ RsmE-binding site with a typical hexaloop (AUGGAA) located on a potential 2-bp stem lies immediately upstream of the phlA SD sequence (Fig.…”