The complete 12 Mb genome and transcriptome of Nonomuraea gerenzanensis with new insights into its duplicated “magic” RNA polymerase

Abstract

In contrast to the widely accepted consensus of the existence of a single RNA polymerase in bacteria, several actinomycetes have been recently shown to possess two forms of RNA polymerases due the to co-existence of two rpoB paralogs in their genome. However, the biological significance of the rpoB duplication is obscure. In this study we have determined the genome sequence of the lipoglycopeptide antibiotic A40926 producer Nonomuraea gerenzanensis ATCC 39727, an actinomycete with a large genome and two rpoB genes, i.e. rpoB(S) (the wild-type gene) and rpoB(R) (the mutant-type gene). We next analyzed the transcriptional and metabolite profiles in the wild-type gene and in two derivative strains over-expressing either rpoB(R) or a mutated form of this gene to explore the physiological role and biotechnological potential of the “mutant-type” RNA polymerase. We show that rpoB(R) controls antibiotic production and a wide range of metabolic adaptive behaviors in response to environmental pH. This may give interesting perspectives also with regard to biotechnological applications.

A Two-Component regulatory system with opposite effects on glycopeptide antibiotic biosynthesis and resistance

“…Inspired by recent work on phylogenetic analysis of cluster-associated StrR-and LuxR-related regulators 22 , we performed a phylogenetic analysis of TCSs from actinomycetes. To this end, we retrieved response regulators and sensory kinases associated with characterized actinobacterial gene clusters from the MiBIG database 23 , well-characterized TCSs from Streptomyces coelicolor 24,25 and the response regulators and sensory kinases identified in the N. gerenzanensis genome 18 (Fig. 8).…”

“…Thus, in its induction mechanism and in the resulting peptidoglycan modification, the mechanism leading to glycopeptide resistance in S. coelicolor resembles that used by pathogenic Enterococcus spp 12,13 . While some glycopeptide producers do contain a vanHAX cassette, either associated with the gene cluster [14][15][16] or elsewhere in the genome 17 , the N. gerenzanensis genome does not contain any such genes 18 . N. gerenzanensis must thus use different strategy(ies) to cope with the self-toxicity of its own product.…”

New Molecular Tools for Regulation and Improvement of A40926 Glycopeptide Antibiotic Production in Nonomuraea gerenzanensis ATCC 39727

“…In the meantime, genome sequencing has revealed the organization of GPA biosynthetic gene clusters (BGCs) in industrially valuable actinobacteria (D' Argenio et al, 2016), including long known GPA-producers (Vongsangnak et al, 2012;Truman et al, 2014;Kusserow and Gulder, 2017;Nazari et al, 2017;Adamek et al, 2018) as well as in novel producing strains (Thaker et al, 2013;Stegmann et al, 2014). Although the global regulation of GPA biosynthesis is still largely unexplored, the pathway-specific regulation controlling the expression of BGCs is being elucidated in model systems (Bibb, 2013).…”

“…The A40926-producing strain, recently re-classified as N. gerenzanensis (Dalmastri et al, 2016), belongs to a still poorly investigated genus of actinobacteria that was only recently identified as an untapped source of novel antibiotics and other bioactive metabolites (Sungthong and Nakaew, 2015). More recently, fully sequenced genomes of N. gerenzanensis (D' Argenio et al, 2016) and of the kistamicin producer Nonomuraea sp. ATCC 55076, previously classified as Actinomadura parvosata subsp.…”

Human Microbiome Acquisition and Bioinformatic Challenges in Metagenomic Studies

“…To overcome 16S rRNA genes sequencing limitations, a shotgun strategy, able to analyze the entire genomic content of a community, can be used. The molecular approach is similar to that used for the analysis of a single bacterial genome [ 79 , 80 ], but in this case sequences from both the host and all the microbes (bacteria, archaea, fungi, and viruses) present in the studied environment are obtained. Consequently, the taxonomic assignment requires highly performing assembly tools and updated databases.…”