A technical platform for generating reproducible expression data from Streptomyces coelicolor batch cultivations
Streptomyces coelicolor, the model species of the genus Streptomyces, presents a complex life cycle of successive morphological and biochemical changes involving the formation of substrate and aerial mycelium, sporulation and the production of antibiotics. The switch from primary to secondary metabolism can be triggered by nutrient starvation and is of particular interest as some of the secondary metabolites produced by related Streptomycetes are commercially relevant. To understand these events on a molecular basis, a reliable technical platform encompassing reproducible fermentation as well as generation of coherent transcriptomic data is required. Here, we investigate the technical basis of a previous study as reported by Nieselt et al. (BMC Genomics 11:10, 2010) in more detail, based on the same samples and focusing on the validation of the custom-designed microarray as well as on the reproducibility of the data generated from biological replicates. We show that the protocols developed result in highly coherent transcriptomic measurements. Furthermore, we use the data to predict chromosomal gene clusters, extending previously known clusters as well as predicting interesting new clusters with consistent functional annotations.
PubMed ID: 21431541
Journal: Adv Exp Med Biol
Citation: Adv Exp Med Biol. 2011;696:3-15. doi: 10.1007/978-1-4419-7046-6_1.
Date Published: 25th Mar 2011
Authors: F. Battke, A. Herbig, A. Wentzel, O. M. Jakobsen, M. Bonin, D. A. Hodgson, W. Wohlleben, T. E. Ellingsen, K. Nieselt
Created: 3rd Dec 2016 at 20:34
Global metabolic switching in Streptomyces coelicolor
Antibiotics are made during the second phase of growth when there is a transition in metabolism from primary to secondary metabolism. Primary metabolism is growth related and involves all the normal cellular activities associated with cell growth and division. Whereas secondary metabolism is non-growth linked and is non-essential but many important activities occur during this phase which help the bacterium survive.
Creators: Jay Moore, Juan-Francisco Martin, Antonio Rodríguez-García, Trond Ellingsen, Øyvind Jakobsen, Per Bruheim, Håvard Sletta, Anders Øverby, Sven Even Borgos, Sunniva Hoel, Alexander Wentzel, Maggie Smith, Louise Thomas, Eriko Takano, Lubbert Dijkhuizen, Rainer Breitling, M. Tauqeer Alam, Anthony Palathingal, R Jansen, Maria Elena Merlo, Morris Swertz, Preben Krabben, Kay Nieselt, Wolfgang Wohlleben, Jens Reuther, David Hodgson, David Rand, David Wild, Elizabeth Wellington, Gregory Challis, Nigel Burroughs, Walid Omara, William Gaze, Brent Kiernan, Roxane Legaie
Contributor: Jay Moore
Investigations: Metabolism of Streptomyces coelicolor (SysMO ST...
Studies: Timeseries 1