|Hassan, Karl - Macquarie University|
|Johnson, Aaron - J. Craig Venter Institute|
|Ren, Qinghu - J. Craig Venter Institute|
|Elbourne, Liam D - Macquarie University|
|Hartney, Sierra - Oregon State University|
|Duboy, Robert - J. Craig Venter Institute|
|Goebel, Neal - Oregon State University|
|Zabriskie, Mark - Oregon State University|
|Paulsen, Ian - Macquarie University|
Submitted to: Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/17/2009
Publication Date: 4/5/2010
Citation: Hassan, K., Johnson, A., Shaffer, B.T., Ren, Q., Kidarsa, T.A., Elbourne, L.H., Hartney, S., Duboy, R., Goebel, N., Zabriskie, M.T., Paulsen, I.T., Loper, J.E. 2010. Inactivation of the GacA response regulator in Pseudomonas fluorescens Pf-5 has far-reaching transcriptomic consequences. Environmental Microbiology. 12(4):899-915. 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 construction of a microarray representing every gene in a biological control organism Pseudomonas fluorescens Pf-5. We used this microarray to determine the effects of a central regulatory gene, gacA, on the expression of all of the other genes in the Pf-5 genome. We learned that gacA influenced the expression of more than 10% of the genes in the Pf-5 genome. Several of the genes regulated by gacA are involved in the production of compounds that are toxic to plant pathogens, including hydrogen cyanide and the antibiotic pyoluteorin. The data also highlighted two new gene clusters that are likely to be unknown secondary metabolites. These new gene clusters can be studied in the future to identify the products they make and the potential role of those products in biological control.
Technical 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 632 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.