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Background  Microbial secondary metabolism is regulated by a complex and mostly-unknown network of global and pathway-specific regulators. A dozen biosynthetic gene clusters for secondary metabolites have been reported in myxobacteria, but a few regulation factors have been identified.    Results  We identified a transcription regulator Esi for the biosynthesis of epothilones. Inactivation of  esi  promoted the epothilone production, while overexpression of the gene suppressed the production. The regulation was determined to be resulted from the transcriptional changes of epothilone genes. Esi was able to bind, probably via the N-terminus of the protein, to an inverted repeat sequence in the promoter of the epothilone biosynthetic gene cluster. The Esi-homologous sequences retrieved from the RefSeq database are all of the Proteobacteria. However, the Esi regulation is not universal in myxobacteria, because the  esi  gene exists only in a few myxobacterial genomes.    Conclusions  Esi binds to the epothilone promoter and down-regulates the transcriptional level of the whole gene cluster to affect the biosynthesis of epothilone. This is the first transcription regulator identified for epothilone biosynthesis.    Electronic supplementary material  The online version of this article (doi:10.1186/s12934-017-0706-9) contains supplementary material, which is available to authorized users.

A bacterial negative transcription regulator binding on an inverted repeat in the promoter for epothilone biosynthesis