ARS | Publication request: The effect of zinc limitation on the transcriptome of Pseudomonas protegens Pf-5

Submitted to: Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 21, 2012
Publication Date: N/A

Interpretive Summary: Biological control provides a promising strategy for managing plant diseases but has not yet been utilized widely in agriculture due, in part, to unexplained variation in its success in managing disease. Our research goals are to identify sources of variation in biological control and devise ways to make it more reliable. We are utilizing new techniques and approaches provided by genomics to meet these goals. In this paper, we describe the use of a microarray to determine the effects of zinc on the expression of all genes in the genome of Pseudomonas protegens Pf-5, a biological control bacterium. We learned that zinc affected biocontrol attributes in Pf-5, most notably reducing the expression of the gene cluster responsible for biosynthesis of the antibiotic 2,4-diacetylphloroglucinol (DAPG) under zinc limitation. Zinc is an important nutrient that is limited in some soil environments, and this study shows that zinc alters the expression of genes important in biological control by a soil bacterium.

Technical Abstract: Zinc is an important nutrient but can be lacking in some soil environments, influencing the physiology of soil-dwelling bacteria. Hence, we studied the global effect of zinc limitation on the transcriptome of the rhizosphere biocontrol strain Pseudomonas protegens Pf-5. We observed that the expression of the putative zinc uptake regulator (Zur) gene was up-regulated, and we mapped putative Zur binding sites in the Pf-5 genome using bioinformatic approaches. In line with the need to regulate intracellular zinc concentrations, an array of potential zinc transporter genes was found to be zinc-regulated. To adapt to low zinc conditions, a gene cluster encoding a non-zinc requiring paralog of zinc-dependent proteins was also significantly up-regulated. Similarly, transcription of genes encoding non-zinc requiring paralogs of ribosomal proteins L31 and L36 was increased by zinc-limitation. A strong transcriptional down-regulation of the putative copper chaperone gene (copZ) was also observed, suggesting interplay between zinc and copper homeostasis. Importantly, zinc also affected biocontrol attributes in Pf-5, most notably reducing the expression of the gene cluster responsible for biosynthesis of the antibiotic 2,4-diacetylphloroglucinol (DAPG) under zinc limitation. This study clearly defines changes to the molecular physiology of Pf-5 that enable it to survive under zinc limitation.