|GOEBEL, NEAL - Oregon State University
|JOHNSON, AARON - J Craig Venter Institute
|KOBAYASHI, DONALD - Rutgers University
|PAULSEN, IAN - Macquarie University
Submitted to: Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/22/2012
Publication Date: 3/1/2013
Citation: Kidarsa, T.A., Shaffer, B.T., Goebel, N.C., Roberts, D.P., Buyer, J.S., Johnson, A., Kobayashi, D.Y., Paulsen, I., Loper, J.E. 2013. Genes expressed by the biological control bacterium Pseudomonas protegens Pf-5 on seed surfaces under the control of the global regulators GacA and RpoS. Environmental Microbiology. 15:716-735.
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 two central regulatory genes, gacA and rpoS, on the expression of all of the other genes in the Pf-5 genome. We determined these effects on bacteria grown in culture and on surfaces of pea seeds. Several of the genes regulated by gacA and rpoS are involved in the production of compounds that are toxic to plant pathogens. Our results show that the genes for production of some of these compounds are expressed by the biological control bacterium on pea seeds. Seeds are commonly infected by fungal pathogens that live in the soil and the biological control organism Pf-5 can protect seeds from infection by these fungi. The results of this study tell us which genes are expressed by Pf-5 on seeds, which helps us identify the particular genes that are required to suppress fungi that infect seeds. This study identified factors influencing the expression of biological control traits on seeds, which is a source of variation in the efficacy of biological control.
Technical Abstract: The GacA/Rsm signal transduction system and the stationary phase sigma factor RpoS have both been shown to affect secondary metabolite production and biological control in Pseudomonas protegens Pf-5 and related strains. Microarray analysis of Pf-5 grown on pea seed surfaces showed that 595 genes are regulated by GacA and 476 by RpoS in this environment. Overall, 897 genes showed significant differential expression in one or both mutants on seed, thus providing evidence for expression of these genes by Pf-5 on seed surfaces. Transcript levels of 262 genes were found to be regulated by RpoS in early stationary phase cultures. Comparison of these data and data from a previous study of the GacA regulon in culture showed that while there was significant overlap between the seed and culture data, the majority of genes were regulated by GacA or RpoS under only one condition, likely due to differing levels of expression in the two conditions. Areas of overlap included some secondary metabolite gene clusters and genes functioning in iron homeostasis. However, genes involved in biofilm formation, cyclic diguanylate (c-di-GMP) signaling, and biosynthesis of some secondary metabolites, including 2,4-diacetylphloroglucinol and a potential novel secondary metabolite, showed much stronger regulation on seed surfaces.