15We present a Penicillium rubens strain with an industrial background in which the four highly expressed 16 biosynthetic gene clusters (BGC) required to produce penicillin, roquefortine, chrysogine and fungisporin 17 were removed. This resulted in a minimal secondary metabolite background. Amino acid pools under 18 steady-state growth conditions showed reduced levels of methionine and increased intracellular aromatic 19 amino acids. Expression profiling of remaining BGC core genes and untargeted mass spectrometry did not 20 identify products from uncharacterized BGCs. This platform strain was repurposed for expression of the 21 recently identified polyketide calbistrin gene cluster and achieved high yields of decumbenone A, B and C. 22 The penicillin BGC could be restored through in vivo assembly with eight DNA segments with short 23 Page 2 of 35 overlaps. Our study paves the way for fast combinatorial assembly and expression of biosynthetic 24 pathways in a fungal strain with low endogenous secondary metabolite burden. 25
Keywords
26Platform strain, Natural products, Penicillium, Biosynthetic gene clusters, Decumbenone, Calbistrin, 27 CRISPR/Cas9, RNP 28 improvement (CSI) have led to accumulation of point mutations 18 that resulted in strains optimized for 52 high ß-lactam yield in large scale fermenters 19 and low unwanted secondary metabolite production. The 53 superior fermentation characteristics of such strains were successfully employed for the production of 54 cephalosporins 20 and, after deletion of the penicillin BGC, also for the heterologous polyketide 55 pravastatin 21 . P. rubens research has led to a full genome sequence 22 and a metabolic model 23 which makes 56 it attractive for future rational strain improvements. In addition, the efficiency of integrating multiple DNA 57 fragments into P. rubens has been increased by utilizing split-marker approaches 24 and the targetable 58 nuclease Cas9 25 . However, direct in vivo recombination for fast construction of different BGC pathway 59 combinations has not yet been demonstrated. Moreover, since the precursors for the biosynthesis of 60 penicillins, α-aminoadipic acid, L-cysteine and L-valine originate from diverse anabolic routes, a careful 61 elucidation of intracellular amino acid pools would be required to assess the impact of CSI on the flexibility 62 of the metabolism to respond to high and low amino acid demands. 63Here, we report on the construction of a P. rubens strain lacking four highly expressed secondary 64 metabolite BGCs resulting in a near to complete secondary metabolite deficient metabolome under the 65 cultivation conditions tested here. We performed genomic and transcriptome analysis, characterized its 66 amino acid profile and demonstrated its suitability for efficient BGC recombination by reconstructing the 67 Penicillin BGC (Pen-BGC) of 17kb by in vivo recombination with 8 DNA fragment with short (110 bp) 68 overlapping flanks. Finally, we utilized this new platform strain for expression of the heterologous 69 calbistrin B...