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Peano, Clelia and Bicciato, Silvio and Corti, Giorgio and Ferrari, Francesco and Rizzi, Ermanno and JP Bonnal, Raoul and Bordoni, Roberta and Albertini, Alberto and Rossi Bernardi, Luigi and Donadio, Stefano and De Bellis, Gianluca (2007) Complete gene expression profiling of Saccharopolyspora erythraea using GeneChip DNA microarrays. [Online journal papers]

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Abstract (english)

Background

The Saccharopolyspora erythraea genome sequence, recently published, presents considerable divergence from those of streptomycetes in gene organization and function, confirming the remarkable potential of S. erythraea for producing many other secondary metabolites in addition to erythromycin. In order to investigate, at whole transcriptome level, how S. erythraea genes are modulated, a DNA microarray was specifically designed and constructed on the S. erythraea strain NRRL 2338 genome sequence, and the expression profiles of 6494 ORFs were monitored during growth in complex liquid medium.

Results

The transcriptional analysis identified a set of 404 genes, whose transcriptional signals vary during growth and characterize three distinct phases: a rapid growth until 32 h (Phase A); a growth slowdown until 52 h (Phase B); and another rapid growth phase from 56 h to 72 h (Phase C) before the cells enter the stationary phase. A non-parametric statistical method, that identifies chromosomal regions with transcriptional imbalances, determined regional organization of transcription along the chromosome, highlighting differences between core and non-core regions, and strand specific patterns of expression. Microarray data were used to characterize the temporal behaviour of major functional classes and of all the gene clusters for secondary metabolism. The results confirmed that the ery cluster is up-regulated during Phase A and identified six additional clusters (for terpenes and non-ribosomal peptides) that are clearly regulated in later phases.

Conclusion

The use of a S. erythraea DNA microarray improved specificity and sensitivity of gene expression analysis, allowing a global and at the same time detailed picture of how S. erythraea genes are modulated. This work underlines the importance of using DNA microarrays, coupled with an exhaustive statistical and bioinformatic analysis of the results, to understand the transcriptional organization of the chromosomes of micro-organisms producing natural products.


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EPrint type:Online journal papers
Anno di Pubblicazione:2007
Key Words:Saccharopolyspora erythraea, gene expression
Settori scientifico-disciplinari MIUR:Area 06 - Scienze mediche > MED/03 Genetica medica
Struttura di riferimento:Dipartimenti > pre 2012 - Dipartimento di Processi chimici dell'Ingegneria
Codice ID:1184
Depositato il:09 Dec 2008
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