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Journal of Bacteriology, February 2009, p. 805-814, Vol. 191, No. 3
0021-9193/09/$08.00+0     doi:10.1128/JB.01311-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Activation of Dormant Bacterial Genes by Nonomuraea sp. Strain ATCC 39727 Mutant-Type RNA Polymerase ^,

Adelfia Talà,¹ Guojun Wang,² Martina Zemanova,¹ Susumu Okamoto,² Kozo Ochi,^2* and Pietro Alifano^1*

Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Via Monteroni, 73100 Lecce, Italy,¹ National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan²

Received 17 September 2008/ Accepted 24 November 2008

There is accumulating evidence that the ability of actinomycetes to produce antibiotics and other bioactive secondary metabolites has been underestimated due to the presence of cryptic gene clusters. The activation of dormant genes is therefore one of the most important areas of experimental research for the discovery of drugs in these organisms. The recent observation that several actinomycetes possess two RNA polymerase β-chain genes (rpoB) has opened up the possibility, explored in this study, of developing a new strategy to activate dormant gene expression in bacteria. Two rpoB paralogs, rpoB(S) and rpoB(R), provide Nonomuraea sp. strain ATCC 39727 with two functionally distinct and developmentally regulated RNA polymerases. The product of rpoB(R), the expression of which increases after transition to stationary phase, is characterized by five amino acid substitutions located within or close to the so-called rifampin resistance clusters that play a key role in fundamental activities of RNA polymerase. Here, we report that rpoB(R) markedly activated antibiotic biosynthesis in the wild-type Streptomyces lividans strain 1326 and also in strain KO-421, a relaxed (rel) mutant unable to produce ppGpp. Site-directed mutagenesis demonstrated that the rpoB(R)-specific missense H426N mutation was essential for the activation of secondary metabolism. Our observations also indicated that mutant-type or duplicated, rpoB often exists in nature among rare actinomycetes and will thus provide a basis for further basic and applied research.

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* Corresponding author. Mailing address for Pietro Alifano: Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Via Monteroni 73100 Lecce, Italy. Phone: 39 0832 298 856. Fax: 39 0832 298 626. E-mail: alifano{at}ilenic.unile.it. Mailing address for Kozo Ochi: National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan. Phone: 81 29 838 8125. Fax: 81 29 838 7996. E-mail: kochi{at}affrc.go.jp

Published ahead of print on 1 December 2008.

Supplemental material for this article may be found at http://jb.asm.org/.

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Journal of Bacteriology, February 2009, p. 805-814, Vol. 191, No. 3
0021-9193/09/$08.00+0     doi:10.1128/JB.01311-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

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