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Open Access Research

Analysis of gene expression in operons of Streptomyces coelicolor

Emma Laing12, Vassilis Mersinias3, Colin P Smith3 and Simon J Hubbard1*

Author Affiliations

1 Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, UK

2 Current Address: School of Biomedical and Molecular Sciences, University of Surrey, Guildford GU2 7XH, UK

3 Functional Genomics Laboratory, School of Biomedical and Molecular Sciences, University of Surrey, Guildford GU2 7XH, UK

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Genome Biology 2006, 7:R46  doi:10.1186/gb-2006-7-6-r46

Published: 2 June 2006

Abstract

Background

Recent studies have shown that microarray-derived gene-expression data are useful for operon prediction. However, it is apparent that genes within an operon do not conform to the simple notion that they have equal levels of expression.

Results

To investigate the relative transcript levels of intra-operonic genes, we have used a Z-score approach to normalize the expression levels of all genes within an operon to expression of the first gene of that operon. Here we demonstrate that there is a general downward trend in expression from the first to the last gene in Streptomyces coelicolor operons, in contrast to what we observe in Escherichia coli. Combining transcription-factor binding-site prediction with the identification of operonic genes that exhibited higher transcript levels than the first gene of the same operon enabled the discovery of putative internal promoters. The presence of transcription terminators and abundance of putative transcriptional control sequences in S. coelicolor operons are also described.

Conclusion

Here we have demonstrated a polarity of expression in operons of S. coelicolor not seen in E. coli, bringing caution to those that apply operon prediction strategies based on E. coli 'equal-expression' to divergent species. We speculate that this general difference in transcription behavior could reflect the contrasting lifestyles of the two organisms and, in the case of Streptomyces, might also be influenced by its high G+C content genome. Identification of putative internal promoters, previously thought to cause problems in operon prediction strategies, has also been enabled.