Metabolic Switches and Adaptations Deduced from the Proteomes of Streptomyces coelicolor Wild Type and phoP Mutant Grown in Batch Culture

Abstract

Bacteria in the genus Streptomyces are soil-dwelling oligotrophs and important producers of secondary metabolites. Previously, we showed that global messenger RNA expression was subject to a series of metabolic and regulatory switches during the lifetime of a fermentor batch culture of Streptomyces coelicolor M145. Here we analyze the proteome from eight time points from the same fermentor culture and, because phosphate availability is an important regulator of secondary metabolite production, compare this to the proteome of a similar time course from an S. coelicolor mutant, INB201 (ΔphoP), defective in the control of phosphate utilization. The proteomes provide a detailed view of enzymes involved in central carbon and nitrogen metabolism. Trends in protein expression over the time courses were deduced from a protein abundance index, which also revealed the importance of stress pathway proteins in both cultures. As expected, the ΔphoP mutant was deficient in expression of PhoP-dependent genes, and several putatively compensatory metabolic and regulatory pathways for phosphate scavenging were detected. Notably there is a succession of switches that coordinately induce the production of enzymes for five different secondary metabolite biosynthesis pathways over the course of the batch cultures. Bacteria in the genus Streptomyces are soil-dwelling oligotrophs and important producers of secondary metabolites. Previously, we showed that global messenger RNA expression was subject to a series of metabolic and regulatory switches during the lifetime of a fermentor batch culture of Streptomyces coelicolor M145. Here we analyze the proteome from eight time points from the same fermentor culture and, because phosphate availability is an important regulator of secondary metabolite production, compare this to the proteome of a similar time course from an S. coelicolor mutant, INB201 (ΔphoP), defective in the control of phosphate utilization. The proteomes provide a detailed view of enzymes involved in central carbon and nitrogen metabolism. Trends in protein expression over the time courses were deduced from a protein abundance index, which also revealed the importance of stress pathway proteins in both cultures. As expected, the ΔphoP mutant was deficient in expression of PhoP-dependent genes, and several putatively compensatory metabolic and regulatory pathways for phosphate scavenging were detected. Notably there is a succession of switches that coordinately induce the production of enzymes for five different secondary metabolite biosynthesis pathways over the course of the batch cultures. Streptomycetes are prolific producers of complex secondary metabolites with pharmaceutically important activities including antibiotics and anti-cancer compounds. In a batch culture growth system, secondary metabolism is often observed when the culture has entered the stationary phase and well after rapid vegetative growth has ceased. Well known examples are the production of actinorhodin (Act) 1The abbreviations used are:ActactinorhodinRedundecylprodigiosinmRNAmessenger RNA. 1The abbreviations used are:ActactinorhodinRedundecylprodigiosinmRNAmessenger RNA. and undecylprodigiosin (Red) in Streptomyces coelicolor (1Bibb M. 1995 Colworth Prize Lecture. The regulation of antibiotic production in Streptomyces coelicolor A3(2).Microbiology. 1996; 142: 1335-1344Crossref PubMed Scopus (185) Google Scholar). This timing implies that secondary metabolism is not simply a consequence of nutrient limitation, but there is an ordered pathway of metabolic and regulatory switches. Many of these have been characterized using a classical genetic approach of generating mutants that no longer produce the antibiotics and studying the genes affected (1Bibb M. 1995 Colworth Prize Lecture. The regulation of antibiotic production in Streptomyces coelicolor A3(2).Microbiology. 1996; 142: 1335-1344Crossref PubMed Scopus (185) Google Scholar, 2Martín J.F. Liras P. Engineering o