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Analysis of gene expression in operons of Streptomyces coelicolor

Laing, E, Mersinias, V, Smith, CP and Hubbard, SJ (2006) Analysis of gene expression in operons of Streptomyces coelicolor GENOME BIOLOGY, 7 (6). ? - ?. ISSN 1474-760X

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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 Zscore 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.

Item Type: Article
Additional Information: © 2006 Laing et al.; licensee BioMed Central Ltd. This is an open acess article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Uncontrolled Keywords: Science & Technology, Life Sciences & Biomedicine, Biotechnology & Applied Microbiology, Genetics & Heredity, ESCHERICHIA-COLI K-12, COMPLETE GENOME SEQUENCE, DEPENDENT ACID RESISTANCE, TRANSCRIPTION TERMINATORS, BACTERIAL GENOMES, PREDICTION, COREGULATION, PROKARYOTES, CONSERVATION, EUKARYOTES
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Divisions: Faculty of Health and Medical Sciences > Microbial and Cellular Sciences
Depositing User: Melanie Hughes
Date Deposited: 24 Feb 2012 14:40
Last Modified: 23 Sep 2013 19:11
URI: http://epubs.surrey.ac.uk/id/eprint/203294

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