Direct Involvement of the Master Nitrogen Metabolism Regulator GlnR in Antibiotic Biosynthesis in Streptomyces

Abstract

Edited by Joel GottesfeldGlnR, an OmpR-like orphan two-component system response regulator, is a master regulator of nitrogen metabolism in the genus Streptomyces. In this work, evidence that GlnR is also directly involved in the regulation of antibiotic biosynthesis is provided. In the model strain Streptomyces coelicolor M145, an in-frame deletion of glnR resulted in markedly increased actinorhodin (ACT) production but reduced undecylprodigiosin (RED) biosynthesis when exposed to R2YE culture medium. Transcriptional analysis coupled with DNA binding studies revealed that GlnR represses ACT but activates RED production directly via the pathway-specific activator genes actII-ORF4 and redZ, respectively. The precise GlnR-binding sites upstream of these two target genes were defined. In addition, the direct involvement of GlnR in antibiotic biosynthesis was further identified in Streptomyces avermitilis, which produces the important anthelmintic agent avermectin. We found that S. avermitilis GlnR (GlnRsav) could stimulate avermectin but repress oligomycin production directly through the respective pathway-specific activator genes, aveR and olmRI/RII. To the best of our knowledge, this report describes the first experimental evidence demonstrating that GlnR regulates antibiotic biosynthesis directly through pathway-specific regulators in Streptomyces. Our results suggest that GlnR-mediated regulation of antibiotic biosynthesis is likely to be universal in streptomycetes. These findings also indicate that GlnR is not only a master nitrogen regulator but also an important controller of secondary metabolism, which may help to balance nitrogen metabolism and antibiotic biosynthesis in streptomycetes.

GlnR Dominates Rifamycin Biosynthesis by Activating the rif Cluster Genes Transcription Both Directly and Indirectly in Amycolatopsis mediterranei

“…In actinomycetes, GlnR was typically viewed as a global nitrogen metabolism regulator before, governing many nitrogen metabolism related processes (Fink et al, 2002;Tiffert et al, 2008;Wang and Zhao, 2009;Wang et al, 2012Wang et al, , 2013Wang et al, , 2014. Recently, several studies have reported that the GlnR homologs in Streptomyces regulate the biosynthesis of some antibiotics, e.g., actinorhodin, avermectin and validamycin (Qu et al, 2015;He et al, 2016). Here our study also shows that the GlnR in A. mediterranei directly controls the rifamycin biosynthesis.…”

“…The phenotypic analyses (Figure 1 and Supplementary Figure S2) showed that, unlike the previous work in Streptomyces (He et al, 2016), the cellular growth under our cultivation conditions was not impaired by glnR deletion at all, which ruled out the impact of the growth factor on gene transcription and on antibiotic production, thus making our conclusions from this study (especially the Figures 1, 2 and Supplementary Figures S2, S3) more reliable. The Supplementary Figure S2B showed that glnR had a significantly lower yield of rifamycin comparing with the wild type U32 when grown in liquid Bennet medium without nitrate, whereas in our previous work, the rifamycin yield of glnR was a little bit higher than that of U32 when grown on Bennet agar plates without nitrate supplementation (Yu et al, 2007).…”

“…Accordingly, the GlnR in actinomycetes is mainly considered as a global nitrogen metabolism regulator. Later, increasing evidences demonstrate that GlnR also regulates the transcription of other genes involved in carbon metabolism, antibiotic biosynthesis and so on (Liao et al, 2015;Qu et al, 2015;Cen et al, 2016;He et al, 2016;You et al, 2017;Liu et al, 2019).…”

Editing streptomycete genomes in the CRISPR/Cas9 age

“…Indeed, the same plasmid has been used by other research groups to edit streptomycete genomes. [34][35][36][37][38] For instance, the same authors later used this toolkit on S. pristinaespiralis to study the regulation of the biosynthesis of the antibiotic pristinamycin I through generation of point-mutations, 34 as well as to increase its production titres through deletion of the cluster-specic transcriptional repressors. 35 In two other instances pKCcas9dO has been used to edit the genome of S. coelicolor: (i) to study the regulation mechanism of the two-component system AfsQ1/Q2 in coelimycin P2 biosynthesis, 36 and (ii) to conrm the involvement of the global transcriptional regulator GlnR in antibiotic biosynthesis regulation.…”

Regulation of specialised metabolites in Actinobacteria – expanding the paradigms

“…This activation is in many instances indirectly mediated by the master response regulator PhoP via signal transduction cascades, which ultimately activate pathway-specific regulators (Rodríguez-García et al, 2007). Similarly, GlnR, the master response regulator for nitrogen metabolism in actinomycetes, which also plays an important role in carbon uptake and metabolism in these organisms (Liao et al, 2015), has been recently found to directly activate pathway-specific regulators of specialised metabolites in several actinomycete genera (Yao et al, 2014;He et al, 2016).…”