Genome-wide analysis of the role of the antibiotic biosynthesis regulator AbsA2 in Streptomyces coelicolor A3(2).

Richard A Lewis,Giselda Bucca,Abdul Wahab,Emma E Laing,Colin P Smith,Carla S Möller-Levet,Andrzej Kierzek,Marie-Joelle Virolle

doi:10.1371/journal.pone.0200673

Abstract

The AbsA1-AbsA2 two component signalling system of Streptomyces coelicolor has long been known to exert a powerful negative influence on the production of the antibiotics actinorhodin, undecylprodiginine and the Calcium-Dependent Antibiotic (CDA). Here we report the analysis of a ΔabsA2 deletion strain, which exhibits the classic precocious antibiotic hyper-production phenotype, and its complementation by an N-terminal triple-FLAG-tagged version of AbsA2. The complemented and non-complemented ΔabsA2 mutant strains were used in large-scale microarray-based time-course experiments to investigate the effect of deleting absA2 on gene expression and to identify the in vivo AbsA2 DNA-binding target sites using ChIP-on chip. We show that in addition to binding to the promoter regions of redZ and actII-orfIV AbsA2 binds to several previously unidentified sites within the cda biosynthetic gene cluster within and/or upstream of SCO3215—SCO3216, SCO3217, SCO3229—SCO3230, and SCO3226, and we relate the pattern of AbsA2 binding to the results of the transcriptomic study and antibiotic phenotypic assays. Interestingly, dual ‘biphasic’ ChIP peaks were observed with AbsA2 binding across the regulatory genes actII-orfIV and redZ and the absA2 gene itself, while more conventional single promoter-proximal peaks were seen at the CDA biosynthetic genes suggesting a different mechanism of regulation of the former loci. Taken together the results shed light on the complex mechanism of regulation of antibiotic biosynthesis in Streptomyces coelicolor and the important role of AbsA2 in controlling the expression of three antibiotic biosynthetic gene clusters.

Highlights

The bacteria of the genus Streptomyces are notable for their ability to undergo morphological differentiation and for their ability to synthesize a wide variety of secondary metabolites
The deletion from S. coelicolor MT1110 of the majority of the absA2 coding sequence coupled with the introduction of a termination codon was expected to confer the classic precocious hyperproduction of antibiotic antibiotic phenotype on MT1110 with regard to Calcium-Dependent Antibiotic (CDA), ACT and red pigmented undecylprodiginines (RED) biosynthesis, [16]
The repression of ACT and RED production by introduction of the heterologously expressed version of absA2 demonstrates that the N-terminally triple-flag tagged version of AbsA2 is capable of complementing the ΔabsA2 and is likely to be a substrate for AbsA1 kinase activity, given that phosphorylated AbsA2 is known to be the functional form of the protein, and it is presumably capable of binding to the actII-orfIV and redZ promoters

Summary

Introduction

The bacteria of the genus Streptomyces are notable for their ability to undergo morphological differentiation and for their ability to synthesize a wide variety of secondary metabolites. Technology, administered by the Pakistan Higher Education Commission (to AW), http://www. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Demuris Ltd. and Certara provided support in the form of salaries for authors RAL and AK, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section

Methods

Results

Conclusion