Transcriptome analysis of the two unrelated fungal β-lactam producers Acremonium chrysogenum and Penicillium chrysogenum: Velvet-regulated genes are major targets during conventional strain improvement programs

Abstract

BackgroundCephalosporins and penicillins are the most frequently used β-lactam antibiotics for the treatment of human infections worldwide. The main industrial producers of these antibiotics are Acremonium chrysogenum and Penicillium chrysogenum, two taxonomically unrelated fungi. Both were subjects of long-term strain development programs to reach economically relevant antibiotic titers. It is so far unknown, whether equivalent changes in gene expression lead to elevated antibiotic titers in production strains.ResultsUsing the sequence of PcbC, a key enzyme of β-lactam antibiotic biosynthesis, from eighteen different pro- and eukaryotic microorganisms, we have constructed a phylogenetic tree to demonstrate the distant relationship of both fungal producers. To address the question whether both fungi have undergone similar genetic adaptions, we have performed a comparative gene expression analysis of wild-type and production strains. We found that strain improvement is associated with the remodeling of the transcriptional landscape in both fungi. In P. chrysogenum, 748 genes showed differential expression, while 1572 genes from A. chrysogenum are differentially expressed in the industrial strain. Common in both fungi is the upregulation of genes belonging to primary and secondary metabolism, notably those involved in precursor supply for β-lactam production. Other genes not essential for β-lactam production are downregulated with a preference for those responsible for transport processes or biosynthesis of other secondary metabolites. Transcriptional regulation was shown to be an important parameter during strain improvement in different organisms. We therefore investigated deletion strains of the major transcriptional regulator velvet from both production strains.We identified 567 P. chrysogenum and 412 A. chrysogenum Velvet target genes. In both deletion strains, approximately 50% of all secondary metabolite cluster genes are differentially regulated, including β-lactam biosynthesis genes. Most importantly, 35-57% of Velvet target genes are among those that showed differential expression in both improved industrial strains.ConclusionsThe major finding of our comparative transcriptome analysis is that strain improvement programs in two unrelated fungal β-lactam antibiotic producers alter the expression of target genes of Velvet, a global regulator of secondary metabolism. From these results, we conclude that regulatory alterations are crucial contributing factors for improved β-lactam antibiotic titers during strain improvement in both fungi.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3663-0) contains supplementary material, which is available to authorized users.

Random Mutagenesis of Filamentous Fungi Strains for High-Yield Production of Secondary Metabolites: The Role of Polyamines

“…An increase in the production of the target SM by 100-to 1000-fold and the elimination of spin-off products under the fermentation conditions in the improved fungal strains ( Figure 2B) are associated with two main molecular events, the upregulation of genes from target BGC and the knockout of genes from alternative BGC [27,33,41,42]. Since the expression of BGC genes is controlled by the pathway-specific regulation [27,43,44], global regulation [45,46], and global regulation of SM [47][48][49][50], the SCI programs are accompanied by changes in such controls.…”

“…In the A. chrysogenum HY strain RNCM 408D [60], the CPC/DAC does not exceed 10-15% [61]. Thus, to increase in SM production is accompanied not only by changes in the expression and regulation of BGCs, but by reprogramming the whole organism, starting with changes in the primary metabolism (for the needs of target SM biosynthesis), ending with changes in the transport and assimilation of nutrients, the ability to assimilate oxygen, adaptation to fermentation conditions, and much more [42]. That is why the improvement of the filamentous fungi strain is a multi-step process, involving alterations in many spheres of the strain's vital activity, and there is no "golden bullet," no one cardinal event that converts WT strain to HY (Figure 1).…”

Omics Approaches Applied to Penicillium chrysogenum and Penicillin Production: Revealing the Secrets of Improved Productivity

“…Some years later, the transcriptome analysis of wild-type and overproducing strains from two unrelated fungal β-lactam producers ( A. chrysogenum and P. chrysogenum ) was carried out [ 61 ]. In this work, P. chrysogenum NRRL 1951 (wild-type) and P2niaD18 (production strain niaD-) were grown in the rich Complete Culture Medium at 27 °C and 120 rpm for three days.…”

Inducible promoters and functional genomic approaches for the genetic engineering of filamentous fungi

“…The comparative transcriptional analysis of the wild-type and production strains from the two antibiotic producers A. chrysogenum and P. chrysogenum (Terfehr et al 2017), revealed that both only distantly related industrial fungi show common transcriptional adaptions towards high-level β-lactam antibiotic biosynthesis. For example, industrial strains from both fungi show an enrichment of differentially regulated genes associated with the supply of precursors and energy for β-lactam production.…”