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University of Groningen

Genetic engineering of Penicillium chrysogenum for the reactivation of biosynthetic pathways

with potential pharmaceutical value

Guzmán Chávez, Fernando

IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below.

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Publication date: 2018

Link to publication in University of Groningen/UMCG research database

Citation for published version (APA):

Guzmán Chávez, F. (2018). Genetic engineering of Penicillium chrysogenum for the reactivation of biosynthetic pathways with potential pharmaceutical value. University of Groningen.

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CHAPTER 3

MECHANISM AND REGULATION

OF SORBICILLIN BIOSYNTHESIS BY

PENICILLIUM CHRYSOGENUM

Fernando Guzmán-Chávez1, Oleksandr Salo1,

Yvonne Nygård1,#, Peter P. Lankhorst3, Roel A.L. Bovenberg2,3,

Arnold J.M. Driessen1,*

1Molecular Microbiology and 2Synthetic Biology and Cell

Engineering, Groningen Biomolecular Sciences and

Biotechnology Institute, University of Groningen, Groningen, The Netherlands

3DSM Biotechnology Center, Delft, The Netherlands

running title: Sorbicillin biosynthesis by Penicillium

Keywords: Penicillium chrysogenum, sorbicillin, polyketide synthase, auto induction, regulator

*Correspondence to arnold J.M. Driessen a.j.m.driessen@rug.nl

#Current address: Biology and Biological Engineering, Industrial

Biotechnology, Chalmers University of Technology, Gothenburg, Sweden

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ABSTRACT

Penicillium chrysogenum is a filamentous fungus that is used to produce β-lactams at an industrial scale. at an early stage of classical strain improvement, the ability to produce the yellow colored sorbicillinoids was lost through mutation. Sorbicillinoids are highly bioactive of great pharmaceutical interest. By repair of a critical mutation in one of the two polyketide synthases in an industrial P. chrysogenum strain, sorbi-cillinoids production was restored at high levels. Using this strain, the sorbicillin biosynthesis pathway was elucidated through gene deletion, overexpression and metabolite profiling. The polyketide synthase en-zymes Sora and SorB are required to generate the key intermediates sorbicillin and dihydrosorbicillin, which are subsequently converted to (dihydro)sorbillinol by the FaD-dependent monooxygenase SorC and into the final product oxosorbicillinol by the oxidoreductase SorD. De-letion of either of the two pks genes not only impacted the overall pro-duction but also strongly reduce the expression of the pathway genes. Expression is regulated through the interplay of two transcriptional regulators; Sorr1 and Sorr2. Sorr1 acts as a transcriptional activator, while Sorr2 controls the expression of sorR1. Furthermore, the sorbi-cillinoids pathway is regulated through a novel autoinduction mecha-nism where sorbicillinoids activate transcription.

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CHAPTER 3

89 INTroDUCTIoN

INTRODUCTION

Sorbicillinoids are a large family of hexaketide metabolites that include more than 90 highly oxygenated molecules. These compounds can be structurally classified into four groups: monomeric sorbicillinoids, bi-sorbicillinoids, tribi-sorbicillinoids, and hybrid sorbicillinoids (Meng et al., 2016). Sorbicillinoids were originally isolated from Penicillium notatum in 1948, but found later also in the culture broths of marine and terres-trial ascomycetes (harned and Volp, 2011). In particular, P. chrysoge-num strain Nrrl1951 has been reported to be a natural source of more than ten sorbicillinoids (Meng et al., 2016). This fungus was the progenitor for the high β-lactam yielding strains that are currently used in industry. These strains were obtained by several decades of classical strain improvement, where an early goal was to eliminate the production of yellow pigments as contaminants of β-lactams. This re-sulted in the loss of sorbicillinoids production through mutagenesis of a key polyketide synthase gene (Salo et al., 2015). recently, the interest in sorbicillinoids was revived because of the wide bioactivity spectrum associated with these molecules and their potential phar-maceutical value. For instance, sorbicathecols a/B inhibits the cyto-pathic effect induced by hIV-1 and influenza virus a (h1N1) in MDCk cells ( Nicoletti and Trincone, 2016) whereas isobisvertinol inhibits lipid droplet accumulation in macrophages, an event associated with the in-itiation of atherosclerosis (koyama et al., 2007; Xu et al., 2016). More-over, the oxidized form of bisvertinol, bisvertinolone, displays a potent cytotoxic effect against hl-60 cells and is an antifungal via inhibition of β(1,6)-glucan biosynthesis (Nicolaou et al., 2000; Du et al., 2009). other sorbicillinoids, such as oxosorbicillinol and dihydrosorbicil linol, were shown to exhibit antimicrobial activity against Staphylococcus aureus and Bacillus subtilis (Maskey et al., 2005).

Despite the wide spectrum of bioactive properties reported for sor-bicillinoids, the biosynthetic pathway of these polyketides has not yet been elucidated. Isotope labelling studies suggested that the hexa-ketide structure of sorbicillinol is assembled by a Claisen type reac-tion involved in carbon-carbon bond formareac-tion (Sugaya et al., 2008; harned and Volp, 2011), whereas Diels-alder and Michael-type reac-tions have been proposed as the most probable mechanism for the formation of sorbicillinoid dimers (Maskey et al., 2005; Du et al., 2009).

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90 M echanism and r egula tion o f sorbicillin bios yn thesis b y Penicillium chry so genum

MaTErIalS aND METhoDS

recently, two polyketide synthases (PkS) have been implicated in the biosynthesis of sorbicillactone a/B in P. chrysogenum E01–10/3. The presumed PkS genes belong to a gene cluster that comprises five addi-tional open reading frames (orFs) (avramović, 2011). Commonly PkS enzymes form the scaffold structure of a molecule that is then fur-ther modified by tailoring enzymes, often encoded by genes localized in the vicinity of the key PkS genes (lim et al., 2012). Indeed, a FaD- dependent monooxygenase has been identified as part of the putative sorbicillin cluster, and this enzyme was shown to convert (2’,3’-dihydro)-sorbicillin into (2’,3’-dihydro)(2’,3’-dihydro)-sorbicillinol (Fahad et al., 2014).

The putative sorbicillinoids gene cluster of industrial P. chrysoge-num strains includes a highly reducing PkS (sorA, Pc21g05080) and a non-reducing PkS (sorB, Pc21g05070) (Salo et al., 2016). The sorA gene was shown to be essential for sorbicillinoids biosynthesis, since its deletion abolishes the production of all related compounds (Salo et al., 2015, 2016). In addition, this cluster harbours five further genes, two genes encoding putative transcription factors (sorR1 and sorR2, Pc21g05050 and Pc21g05090, respectively), a transporter protein (sorT, Pc21g05100), a monooxygenase (sorC, Pc21g05060) and an ox-idase (sorD, Pc21g05110). a recent study in Trichoderma reesei indi-cates that homologous transcription factors are involved in the regu-lation of sorbicillinoid biosynthesis in this fungus (Derntl et al., 2016), but the exact mechanism of regulation remained obscure. here, we have resolved the biosynthetic pathway of sorbicillinoids biosynthesis and its regulation by metabolic and expression profiling of individual gene knock-out mutants. The data shows that Sorr1 is a transcrip-tional activator, whose expression is controlled by the second regula-tor Sorr2. Furthermore, transcription is regulated through an autoin-duction mechanism by sorbicillinoids, the products of the pathway. MATERIALS AND METHODS

STRAINS, MEDIA AND GROWTH CONDITIONS.

Penicillium chrysogenum DS68530 was kindly provided by DSM Sinochem Pharmaceuticals (Delft, The Netherlands). all gene deletion and overex-pression strains were derived from DS68530res13 (Sorb407) described

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CHAPTER 3

91 MaTErIalS aND METhoDS

by Salo et al. 2016, which is a derivative of DS68530. The overexpres-sion strains used in the feed experiments were derived of DS68530 (Table S1). Conidiospores immobilized on rice were inoculated in yGG medium for 48 h hour to produce fungal protoplasts or for gDNa ex-traction, and for 24 h to produce young mycelium used as pre-culture inoculum for production fermentations. after pre-culture, the inoculum was diluted seven times in SMP medium (secondary metabolite pro-duction medium, (ali et al., 2013) and cells were grown for up to 5 days in shaken flasks at 25 °C and 200 rpm. after 3 and 5 days, samples of the culture medium were collected for rNa extraction and metabolite profile analysis. When indicated, phleomycin agar medium (Snoek et al., 2009) supplemented with 60 µg/ml phleomycin was used for selection and strain purification. Selected transformants were placed on r-agar for sporulation during 5 days, whereupon the conidiospores were used to prepare rice batches for long-term storage (kovalchuk et al., 2012).

CONSTRUCTION OF GENE DELETION AND OVEREXPRESSION STRAINS

Gene deletion and overexpression mutants were build using the Gate-way Technology (Invitrogen, USa). For creation of deletion strains, 5’ and 3’ regions of each target genes (Pc21g05050 (sorR1), Pc21g05060 (sorC), Pc21g05070 (sorB), Pc21g05080 (sorA), Pc21g05090 (sorR2), Pc21g05100 (sorT) and Pc21g05110 (sorD)), were amplified from gDNa of strain DS68530. all primers used in this study are listed in Table S2. The resistance marker gene (ble) for phleomycin was amplified from

pJak-109 (Pohl et al., 2016). Phusion hF polymerase (Thermo Fisher Scientific, USa) was used to amplify all the DNa parts used. The ble gene was placed under control of pcbC promoter of P. chrysogenum. all the fragments generated were cloned in the respective donor vectors PDoNr P4-P1r, pDoNr2r-P3 and pDoNr 221 using BP Clonase II enzyme mix (Invitrogen, USa), and transformed into E. coli Dh5α, where plasmids were selected for with kanamycin. Next, the constructs were used in an in vitro recombination reaction with the pDEST r4-r3 vector employing lr Clonase II Plus enzyme mix ( Invitrogen, USa). Following transformation to E. coli Dh5α, correct constructs were selected for with ampicillin.

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92 M echanism and r egula tion o f sorbicillin bios yn thesis b y Penicillium chry so genum

MaTErIalS aND METhoDS

The donor vectors containing the 5’ flank were used to generate the 5’ flanks in the overexpression cassettes. The 3’ flank was generated from amplified homologous regions that were located before and af-ter the start codon of each gene (sorR1; sorR2). The pcbC (isopenicillin N synthase) gene promoter of P. chrysogenum was used to induce ex-pression and was inserted between the two flanks selected. To build the DNa fragment that contains the phleomycin resistant cassette, the ble gene was amplified from plasmid pFP-phleo-122 (Polli et al., unpublished) and the pcbC promoter which was ordered as a synthetic gene (gBlock) (IDT, USa). The ble gene in the phleomycin resistance cassette (promoter, gene and terminator) is under control of the gndA (6-phospho- gluconate dehydrogenase) promoter of Aspergillus nidu-lans (Polli et al., 2016). Next, the two fragments were fused by overlap PCr, as described by Nelson & Fitch (2011).

FUNGAL TRANSFORMATION

Protoplasts were isolated from P. chrysogenum as described previ-ously (kovalchuk et al., 2012). For all transformations, 5 µg of plasmid DNa was linearized with a suitable restriction enzyme, whereupon transformation was done as described by Weber et al. (Weber et al., 2012). Screening of transformants was performed by colony PCr us-ing the Phire Plant Direct PCr kit (life Technologies, USa). Positive transformants were purified by three rounds of sporulation on r-agar medium. Transformants were further validated by sequencing inte-gration regions amplified from gDNa.

SOUTHERN BLOT ANALYSIS

a DNa fragment between 0.7 and 0.1 kb from the upstream or down-stream region of every gene was amplified and used as a probe for Southern blot analysis (Figure S1). The probes were labelled with the highPrime kit (roche applied Sciences, The Netherlands). about 15 µg of gDNa, previously digested with suitable restriction enzymes was separated by electrophoresis on an 0.8 % agarose gel. The gel was equilibrated in 20× saline-sodium citrate (SSC) buffer (3 M NaCl;

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CHAPTER 3

93 MaTErIalS aND METhoDS

0.3 M C6h5Na3o7; ph 7) and the DNa was transferred overnight to a positively charged nylon membrane (Zeta-Probe, Biorad, USa). Sub-sequently, the membrane was incubated overnight with the labelled probe(s). For detection, the membrane was treated with anti-DIG fab fragment alkaline phosphatase and the CDP-Star chemiluminescent substrate (roche applied Sciences, The Netherlands). The signal was measured with a lumi-Imager (Fujifilm laS-4000, Japan).

qPCR ANALYSIS

Mycelium of strains grown for 3 and 5 days in SMP medium was har-vested and disrupted in a FastPrep FP120 system (Qbiogene, USa) to isolate total rNa. The extraction was performed with the Trizol ( Invitrogen, USa) method and the total rNa obtained was purified with the Turbo DNa-free kit (ambion, USa). rNa integrity was checked on a 2 % agarose gel and the rNa concentration was measured using a Nanodrop ND-1000 device (ISoGEN, The Netherlands). To synthe-size cDNa, 500 ng of rNa was used per reaction using iScript cDNa synthesis kit (Biorad, USa). The primers used were described previ-ously (Salo et al., 2016). The γ-actin gene (Pc20g11630) was used as a control for normalization (Nijland et al., 2010). The SensiMIx SyBr hi-roX (Bioline, australia) was used as master mix for the qPCr in a Miniopticon system (Biorad,USa). The following thermocycler condi-tions were employed: 95 °C for 10 min, followed by 40 cycles of 95 °C for 15 s, 60 °C for 30 s, and 72 °C for 30 s. Measurements were ana-lyzed with the Bio-rad CFX manager program in which the Ct (thresh-old cycles) values were determined by regression. To determine the specificity of the qPCr reactions, melting curves were generated. The

analysis of the relative gene expression was performed with 2-ΔΔCT

method ( livak and Schmittgen, 2001). The expression analysis was done for two biological samples with at least two technical replicates.

METABOLITE ANALYSIS

Strains were grown in SMP medium and supernatant was collected after 3 and 5 days. Samples were centrifuged for 5 min at 14000 rpm

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94 M echanism and r egula tion o f sorbicillin bios yn thesis b y Penicillium chry so genum rESUlTS

to remove the mycelium whereupon 1 ml of the supernatant fraction was filtered with a 2 µm-pore polytetrafluoroethylene (PTFE) syringe filter and stored at −80 °C. lC-MS analysis was done as described pre-viously (Salo et al., 2016). Metabolite analysis was performed with two biological samples with two technical duplicates.

OTHER METHODS

For the feeding experiments with sorbicillinoids, the parental strain DS68530 and its derivatives ΔsorR1, ΔsorR2, oEsorr1_68530 and oEsorr2_68530, were grown in yGG medium. after 24 hours, the inoculum of 3 ml was transferred into a 100 ml shake flask, supple-mented with 20 ml of fresh SMP and 2 ml of filtered supernatant that was obtained from a 3 days old culture of the sorbicillinoids produc-ing strainDS68530res13, also grown in SMP. Controls received su-pernatant of the DS68530 strain, a non sorbicillinoids producer. Sam-ples for expression and metabolite analysis were taken at day 1, 3 and 5 of growth.

RESULTS

METABOLIC PROFILING OF STRAINS WITH INDIVIDUAL DELETIONS OF THE SORBICILLINOIDS BIOSYNTHESIS GENES

P. chrysogenum strain DS68530res13 produces high levels of sorbicilli-noids causing yellow pigmentation of the culture broth. This strain is de-rived from strain DS68530 as described previously (Salo et al., 2016). The proposed sorbicillin biosynthetic gene cluster (Figure 1a) includes the previously characterized polyketide synthase gene sorA (Pc21g05080), a second polyketide synthase (Pc21g05070, sorB), two transcriptional factors (Pc21g05050, sorR1; Pc21g05090, sorR2), a transporter protein (Pc21g05100, sorT), a monooxygenase (Pc21g05060, sorC) and an oxido-reductase (Pc21g05110, sorD). These genes were individually deleted and metabolic profiling using lC-MS was performed on the superna-tant fractions of cultures of the respective strains. Mass spectra were searched for the previously identified sorbicillinoids-related compounds

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CHAPTER 3

95 rESUlTS

as well as potential new molecules. Furthermore, the expression of the aforementioned genes was analyzed by qPCr to exclude possible polar effects of the gene deletions and to assess the impact of the de-letion of the two putative regulators on the expression of the sorbicil-linoids gene cluster.

In the ΔsorA mutant which lacks the highly reducing polyketide syn-thase, no sorbicillinoids could be detected in the culture supernatant (Figure 2B) confirming our earlier observations (Salo et al., 2016). also in the ΔsorB mutant, which lacks the non-reducing polyketide syn-thase, sorbicillinoids production was completely abolished (Figure 2B). These data are consistent with the notion that Sora and SorB are re-sponsible for the formation of the core (dihydro-) sorbicillin structure. The unknown compound [13] was present at elevated levels in both

the ΔsorA and ΔsorB mutants as compared to the parental strain and thus is most likely not related to sorbicillins. This compound has a

re-tention time (rT) of 14.21 minutes, m/z [h]+ of 304.1652 and a

calcu-lated empirical formula C16h21o3N3 (Figure 2B). all the other unknown compounds listed in Figure 2 appear to be associated with the sorb-icillinoids biosynthetic pathway. Importantly, both in the ΔsorA and ΔsorB mutants, none of the cluster genes except the sorR1 gene were expressed (Figure 1B).

Next, the role of the individual genes encoding the enzymes of the pathway were analyzed. Deletion of the monooxygenase gene sorC resulted in a 1.3 times increase of dihydrosorbicillinol [4]. The ΔsorC mutant showed lower levels of sorbicillin and sorbicillinol, which is consistent with the proposed role of SorC protein in the oxidative dea-romatisation of sorbicillin [1] into sorbicillinol [3*] (Fahad et al., 2014). In this strain we also noted an upregulation of the sorB gene and the partial down regulation of the rest of the cluster (Figure 1B). The main compound produced after 3 days in the ΔsorD strain, which lacks the putative oxidoreductase, was sorbicillinol [3;3*]. after 5 days, elevated

levels of compound [15] with the m/z [h]+ of 293.1493 was also noted.

oxosorbicillinol [5*] with an empirical formula of C14h16o5 and m/z

[h]+ of 265.1069 was not detected in this strain, which suggests that

SorD is involved in the conversion of sorbicillinol into oxo sorbicillinol. The ΔsorD strain showed a slight overexpression (0.6 times higher)

of the sorB gene while the other genes of the pathway were about 2-fold downregulated (Figure 1B). The ΔsorT mutant which lacks the

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96 M echanism and r egula tion o f sorbicillin bios yn thesis b y Penicillium chry so genum rESUlTS

A) sorR1 sorC sorB sorA sorR2 sorT sorD

B)

sorR1 sorC sorB sorA sorR2 sorT sorD

sorR1

sorR1 sorC sorB sorA sorR2 sorT sorD ∆sorC 0 1 2 3 4 5 6 7 8 9 10 ∆sorA

sorR1 sorC sorB sorA sorR2 sorT sorD

sorR2

sorR1 sorC sorB sorA sorR2 sorT sorD ∆sorT

sorR1 sorC sorB sorA sorR2 sorT sorD ∆sorD Pc21g05050 Pc21g05060 Pc21g05070 Pc21g05080 Pc21g05090 Pc21g05100 Pc21g05110sorB 0 1 2 3 4 5 6 7 8 9 10 C) 0 1 2 3 4 5 6 7 8 9 10 Fold change Fold change OE_sorR2

sorR1 sorC sorB sorA sorR2 sorT sorD sorR1 sorC sorB sorA sorR2 sorT sorD

OE_sorR1 F old change 0,000 0,000 0,002 0,008 0,031 0,125 0,500 2,000 8,000 32,000 128,000 512,000 2.048,000 8.192,000 0,002 0,008 0,031 0,125 0,500 2,000 8,000 32,000 128,000 512,000 2.048,000 8.192,000 0.5 2 8 32 128 512 2048 8192 0

Figure 1. Relative expression of the genes of the sorbicillinoids biosynthesis

gene cluster. A) Schematic representation of the gene cluster: Pc21g05050 (sorR1; transcriptional factor), Pc21g05060 (sorC; monooxigenase), Pc21g05070 (sorB; non-reduced polyketide synthase), Pc21g05080 (sorA; highly reduced polyketide synthase), Pc21g05090 (sorR2; transcriptional factor), Pc21g05100 (sorT; MFS transporter) and Pc21g05110 (sorD; oxidase). B) Quantitative Real Time PCR analysis in sorbicillinoids gene cluster expression in strains with in-dividual deleted sorA, sorB, sorC, sorD and sorT, C) sorR1 and sorR2 genes. D) qPCR analysis in strains and overexpressed sorR1 and sorR2. Samples were taken at day 1 (gray bars), 3 (white bars) and 5 (black bars). Data shown as fold change relative to P. chrysogenum DS68530Res13 strain.

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97 rESUlTS

putative transporter showed a similar gene expression as the paren-tal strain with only minor changes in sorB and sorR2 expression. In this strain, the production of sorbicillinoids shifted mostly towards tet-rahydrobisvertinolone [9] and the compound with an empirical for-mula C15h20o4N2 [15].

Summarizing, our data suggests that the monooxygenase SorC is involved in the oxidative dearomatisation of sorbicillin [1] into sorb-icillinol [3*], and that the oxidoreductase SorD converts sorbsorb-icillinol [3;3*] into oxosorbicillinol [5*]. No clear role can be attributed to the transporter SorT. Furthermore, the individual deletion of the biosyn-thesis genes also impacts the regulation of the pathway.

DELETION AND OVEREXPRESSION OF THE REGULATORY GENES SORR1 AND SORR2

The sorbicillinoids biosynthetic gene cluster contains two genes en-coding putative regulators, i.e. sorR1 and sorR2. The deletion of sorR1 abolished the expression of the entire sorbicillin biosynthesis gene cluster and consequently all sorbicillinoid related compounds were absent in this strain (Figure 1C, 2B). The deletion of sorR2 impacted the expression after 3 days (Figure 1C), while after 5 days, the ex-pression profiles were equal or even higher than in the parental strain (Figure 1C). Intriguingly, despite the biosynthetic genes being ex-pressed, hardly any sorbicillinoids were present in the culture broth of the ΔsorR2 strain, except for very low levels of dihydrosorbicillinol [4] (Figure 2B). These data suggested that Sorr1 is essential for the reg-ulation of sorbicillinoid biosynthesis, whereas the absence of Sorr2 results in a delayed expression of the pathway genes.

overexpression of sorR1 (OEsorR1) or sorR2 (OEsorR2) resulted in el-evated levels of these regulators in the early stages of the cultivation (Figure 1D). In the OEsorR1 strain, this also substantially elevated the ex-pression of the other pathway genes which suggests that Sorr1 acts as a transcriptional activator. Concomitantly, the overexpression of sorR1 massively increased the sorbicillinoid production (Figure 2B). In con-trast, in the oEsorr2 mutant the expression of nearly all the genes of the sorbicillinoids cluster was strongly reduced, except for sorR1 expres-sion which was increased. Consequently, production of all sorbicillinoid

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98 M echanism and r egula tion o f sorbicillin bios yn thesis b y Penicillium chry so genum rESUlTS M ax M in DS68530Re s13 N o Co m po un d N am e Fo rm ul a Ac qu ire d RT [M +H ] + (m in ) 3 5 3 5 3 5 3 5 3 5 3 5 3 5 3 5 3 5 3 5 1 So rb ic ill in C14 H16 O3 23 3, 11 74 30 ,8 4 0, 12 0, 37 0, 00 0, 00 0, 00 0, 35 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 09 0, 19 0, 23 0, 26 1, 03 0, 95 0, 00 0, 00 2 Di hy dr os or bi ci lli n C14 H18 O3 23 5, 13 29 32 ,0 1 0, 00 0, 00 0, 00 0, 00 0, 00 0, 14 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 03 0, 04 0, 00 0, 00 3 So rb ic ill in ol C14 H16 O4 24 9, 11 19 21 ,0 1 1, 82 11 ,1 3 0, 00 0, 00 0, 12 0, 14 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 86 0, 85 4, 42 6, 61 23 ,6 3 14 ,1 2 0, 00 0, 00 4 Di hy dr os or bi ci lli no l C14 H18 O4 25 1, 12 74 22 ,6 6 0, 04 8, 95 0, 00 0, 00 0, 04 11 ,8 7 0, 00 0, 00 0, 00 0, 00 0, 01 0, 25 2, 00 13 ,6 5 0, 05 14 ,9 8 10 ,8 5 38 ,4 3 0, 00 0, 00 5 O xo so rb ic ill in ol C14 H16 O5 26 5, 10 69 19 ,3 4 0, 02 0, 29 0, 00 0, 00 0, 00 0, 04 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 35 0, 00 0, 05 0, 61 0, 38 0, 00 0, 00 2* Di hy dr os or bi ci lli n* C14 H18 O3 23 5, 13 29 47 ,0 8 0, 00 0, 00 0, 00 0, 00 0, 00 1, 82 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 3* So rb ic ill in ol * C14 H16 O4 24 9, 11 19 22 ,3 3 14 ,4 7 19 ,5 1 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 05 0, 00 26 ,7 2 26 ,7 7 83 ,8 6 27 ,7 2 0, 00 0, 00 4* Di hy dr os or bi ci lli no l* C14 H18 O4 25 1, 12 74 24 ,9 5 0, 16 9, 88 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 04 7, 12 7, 61 0, 32 13 ,3 2 23 ,2 3 23 ,4 8 0, 00 0, 00 5* O xo so rb ic ill in ol * C14 H16 O5 26 5, 10 69 27 ,4 3 0, 08 2, 45 0, 00 0, 00 0, 00 0, 11 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 1, 84 1, 40 0, 00 0, 00 6 Bi so rb ic ill in ol C28 H32 O8 49 7, 21 64 29 ,0 8 0, 00 0, 17 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 30 1, 53 0, 91 0, 00 0, 00 7 Bi sv er tin ol on C28 H32 O9 51 3, 21 10 32 ,9 7 0, 02 2, 12 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 35 ,3 7 15 ,1 2 0, 00 0, 00 8 Di hy dr ob is ve rti no lo ne C28 H34 O9 51 5, 22 69 33 ,5 0 0, 00 1, 54 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 03 0, 00 0, 00 3, 78 6, 98 0, 00 0, 00 9 Te tr ah yd ro bi sv er tin ol on e C28 H36 O9 51 7, 24 24 33 ,7 2 0, 00 0, 24 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 19 17 ,3 4 0, 00 0, 00 1, 24 11 ,6 8 0, 00 0, 00 10 Un kn ow n C12 H14 O3 20 7, 10 15 23 ,9 8 0, 87 0, 19 0, 00 0, 00 0, 03 0, 48 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 15 0, 00 0, 22 0, 02 3, 29 2, 27 0, 00 0, 00 11 Un kn ow n C11 H12 O3 19 3, 08 60 21 ,3 0 7, 67 1, 53 0, 00 0, 00 0, 33 2, 86 0, 00 0, 00 0, 00 0, 00 0, 00 0, 02 6, 18 0, 00 14 ,4 9 0, 05 12 ,0 3 7, 57 0, 00 0, 00 12 Un kn ow n C12 H17 O N 19 2, 13 82 14 ,0 4 0, 22 0, 53 0, 00 0, 00 0, 05 0, 05 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 1, 18 2, 56 0, 81 1, 41 3, 64 3, 02 0, 00 0, 00 13 Un kn ow n C16 H21 O3N 3 30 4, 16 52 14 ,2 1 0, 00 0, 66 0, 00 4, 01 0, 00 5, 58 0, 29 4, 27 0, 71 1, 12 0, 10 0, 38 0, 01 0, 00 0, 03 0, 42 0, 00 1, 26 0, 12 1, 13 14 Un kn ow n C15 H20 O5N 2 30 9, 14 41 15 ,8 6 0, 07 3, 64 0, 00 0, 00 0, 00 0, 05 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 18 2, 66 7, 83 12 ,5 5 0, 00 0, 00 15 Un kn ow n C15 H20 O4N 2 29 3, 14 93 17 ,5 5 0, 01 12 ,0 1 0, 00 0, 00 0, 01 1, 25 0, 00 0, 00 0, 00 0, 00 0, 00 0, 36 1, 86 26 ,0 0 0, 04 33 ,6 5 20 ,3 2 36 ,8 3 0, 00 0, 00 16 Un kn ow n C22 H40 O15 N8 65 7, 26 78 35 ,8 9 0, 30 7, 49 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 57 4, 67 32 ,6 8 25 ,3 4 0, 00 0, 00 17 Un kn ow n C11 H10 O5 22 3, 06 01 15 ,4 4 0, 00 0, 26 0, 00 0, 00 0, 00 0, 22 0, 00 0, 00 0, 00 0, 00 0, 00 0, 02 0, 01 0, 56 0, 02 5, 00 2, 34 6, 25 0, 00 0, 00 18 Un kn ow n C14 H18 O5 26 7, 12 41 17 ,0 6 0, 03 0, 87 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 03 0, 17 1, 09 2, 90 4, 07 0, 00 0, 00 19 Un kn ow n C12 H32 O15 N8 52 9, 20 60 28 ,2 1 0, 00 9, 22 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 0, 00 17 ,4 3 29 ,9 3 0, 00 0, 00 Δ so rR 1 Δ so rC Δ so rB Δ so rA Δ so rR2 Δ so rT Δ so rD OEsorR1 OEsorR2 O O O H O O OH H O H O O CH 3 OH H3 C HO CH3 Sorbicillin (1) 2'-3'Dihydrosorbicillin (2,2*) O CH 3 OH H3 C O H 3 C OH OH CH 3 O H3 C HO H 3 C OH Oxosorbicillinol (5,5*) O O H3 C O H3 C O CH3 CH 3 CH3 CH 3 OH OH OH HO OH Bisvertinolon (7) O H3 C OH O HO CH3 OH H CH3 CH3 OH HO CH 3 O CH 3 O Dihydrobisvertinolone (8) O H3 C OH O HO CH 3 OH H CH 3 CH 3 OH HO CH3 O CH 3 O Tetrahydrobisvertinolone (9) Sorbicillinol (3,3*) 2'-3'Dihydrosorbicillin (4,4*) CH 3 CH 3 CH 3 H3 C H3 C H3 C Bisorbicillinol (6) A) B) Response r atio

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99 rESUlTS

related compounds was reduced. These data suggest that Sorr2 is in-volved in a complex mechanism of regulation, and likely acts in concert with Sorr1 which is a transcriptional activator of the pathway.

SORBICILLINOIDS ACTIVATE GENE EXPRESSION

The observation that deletion of the PkS enzymes Sora and SorB, and consequently a loss in sorbicillinoids production, causes a marked re-duction in the expression levels of the biosynthesis genes suggests that sorbicillinoids influence the expression of the pathway through an auto induction regulatory process. To test this hypothesis, a culture of strain DS68530, which itself does not produce sorbicillinoids be-cause of the mutation in Sora was fed with a sorbicillinoids containing spent medium derived from the DS68530res13 strain. This resulted in highly increased expression of all sorbicillinoids biosynthetic genes (Figure 3a), except for the two regulatory genes, the expression of which remained unchanged. as a control, the cells were fed with su-pernatant derived from the non-sorbicillin producing strain DS68530, and this had no impact on the expression of the sorbicillinoids gene cluster. These data suggest that the sorbicillinoids biosynthetic gene cluster is regulated through an auto induction mechanism by which the products of the pathway, the sorbicillinoids, stimulate the expres-sion of the pathway genes.

To examine the auto induction mechanism in greater detail, the effect of sorbicillinoids addition was also tested for the ΔsorR1 and ΔsorR2 strains, and strains overproducing sorR1 (OEsorR1) or sorR2 (OEsorR2) in the genetic background of the non-sorbicillin producing

Figure 2. A) Sorbicillinoids related compounds detected in this study. B)

Re-sponse ratio of the sorbicillinoids concentrations in the culture broth of indi-cated sorbicillin producing P. chrysogenum strains. Reserpine was used as inter-nal standard for normalization. Compounds were detected after 3 and 5 days of growth. The mass to charge ratio (m/z) of the protonated metabolites, their empirical formulas and retention time (RT) are indicated. Structures of sor-bicillin related compounds detected in this study. (*) Indicates an isomer of the known sorbicillinoids.

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100 M echanism and r egula tion o f sorbicillin bios yn thesis b y Penicillium chry so genum rESUlTS

strain DS68530. Expression of the cluster genes remained unaffected in the ΔsorR1 and ΔsorR2 strains when cells were grown in the pres-ence of sorbicillinoids (data not shown, Figure 3B). overproduction of sorR1 resulted in the elevated expression of the pathway genes which was further stimulated by the presence of sorbicillinoids in the culture medium (Figure 3C). a similar result was obtained with the overexpres-sion of sorR2, albeit the effect of sorbicillinoids was at least two orders of magnitude lower (Figure 3D). It should be noted that sorT in the OEsorR2 strain was highly overexpressed. This gene lies downstream of sorR2 and due to strain construction, it is no longer expressed from its endogenous promoter but controlled by the strong gndA promoter

B)

sorR1 sorC sorB sorA sorR2 sorT sorD

1 2 4 8 16 32 64 128 256 512 1024 OEsorR1_68530 F old change A) D) C) 1 2 4 8 16 32 64 128 256 512 1024 0.5

sorR1 sorC sorB sorA sorR2 sorT sorD

1 2 4 8 16 32 64 128 256 512 1024

sorR1 sorC sorB sorA sorR2 sorT sorD

DS68530 ∆sorR2 0,01 0,02 0,03 0,06 0,13 0,25 0,50 1,00 2,00 4,00 8,00 16,00 32,00 64,00 128,00 256,00 512,00 1024,00 0,25 0,50 1,00 2,00 4,00 8,00 16,00 32,00 64,00 128,00 256,00 512,00 1024,00 1 2 4 8 16 32 64 128 256 512 1024 0.0

sorR1 sorC sorB sorA sorR2 sorT sorD

OEsorR2_68530

Figure 3. Relative expression of the sorbicillinoids cluster genes in presence

(black bars) and absence (white bars) of sorbicillinoids in the growth medium. Strains: A) DS68530, B) ΔsorR2, C) OEsorR1_68530 and D) OEsorR2_68530. Samples were taken after 3 days of growth. Data shown as fold change relative to P. chrysogenum DS68530 strain.

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101 DISCUSSIoN

(Polli et al., 2016). Taken together, these data suggest that sorbicilli-noids autoinduce the sorbicillisorbicilli-noids biosynthetic pathway in a process that requires the combined activity of the transcriptional regulators Sorr1 and Sorr2.

DISCUSSION

P. chrysogenum produces large amounts of sorbicillinoids. In a previ-ous study, we have identified one of the polyketide synthases (Sora) involved in this process (Salo et al., 2016). To resolve the biosynthetic mechanism of sorbicillinoids production, each of the genes of the pu-tative cluster was individually deleted and analyzed by metabolic pro-filing. our data indicates that the two polyketide synthase genes, sorA and sorB, are both required for sorbicillinoids production. our metabolic profile analysis did not reveal possible intermediate products of the polyketide synthases. however, it has previously been suggested that these two proteins are responsible for the synthesis of the basic hexa-ketide scaffold (Figure 4a) (harned and Volp, 2011; Fahad, 2014). Bio-synthesis of sorbicillin or dihydrosorbicillin depends of the functionality of the enoylreductase (Er) domain of Sora, while the methylation of the hexaketide derived from Sora, prior to the cyclization, is catalyzed by SorB. our deletion analysis further suggests that SorC, a monooxy-genase, is needed for the conversion of dihydrosorbicillin [2*] and sorb-icillin [1] into dihydrosorbsorb-icillinol [4*] and sorbsorb-icillinol [3*], respectively, which confirms previous observations on the biochemical characteri-zation of this enzyme (Fahad et al., 2014). Nevertheless, SorC is appar-ently not the only enzyme or mechanism involved in this conversion step as low amounts of likely tautomer forms of (dihydro)sorbicillinol [4;3] (harned and Volp, 2011) were still detected in the supernatant of the ΔsorC mutant. In the ΔsorD strain, sorbicillinol [3;3*] accumu-lated while oxosorbicillinol [5*] could not be detected. This suggested that SorD is an oxidase that converts sorbicillinol into oxo sorbicillinol [5*], which is also a stable compound. although low amounts of the potential tautomer [5] have been previously detected (Maskey et al., 2005), this molecule might be the result of the spontaneous oxidation of sorbicillin (Bringmann et al., 2005). Furthermore, we could not de-tect dihydrobisvertinolone [8] and tetrahydrobisvertinolone [9] in the

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102 M echanism and r egula tion o f sorbicillin bios yn thesis b y Penicillium chry so genum DISCUSSIoN

supernatant, which is in line with the proposed function of SorD as the product oxosorbicillinol is a precursor for bisvertinolone synthesis (abe et al., 2002). Deletion of the gene specifying the transporter SorT only marginally affected sorbicillinoids production and thus no clear transport function could be assigned to this protein. Summarizing, the functional assignment of the various gene products resulted in a bio-synthetic scheme depicted in Figure 4. a similar pathway was recently constructed for Trichoderma reesei (astrid r. Mach-aigner, personal communication).

To understand the mechanism of regulation of the pathway, we ana-lyzed the effect of the deletion and overexpression of the two puta-tive transcriptional regulators, sorR1 and sorR2 that are part of the gene cluster. The data indicate that Sorr1 is needed for the transcrip-tional activation of sorbicillinoids gene cluster. In the sorR1 deletion strain, the expression of all biosynthetic genes was completely abol-ished and consequently, sorbicillinoids production was eliminated. In the overexpression strain, cluster genes were upregulated causing an earlier onset of sorbicillinoids biosynthesis. SorR2 appears to fulfil a more complex role. Deletion of sorR2 caused a later onset of the ex-pression of the sorbicillinoids genes, which explains the low amounts of sorbicillinoids that are still detected in that strain. In the sorR2 over-expression strain, the transcriptional levels of sorR1 were strongly en-hanced, while the expression of the pathway genes were strongly re-duced at later stages of growth. Moreover, sorD was not expressed and overall sorbicillinoids production was abolished. This observa-tion suggests a complex mechanism of regulaobserva-tion in which Sorr1 and Sorr2 cooperate at the protein level. While the data is consistent with a model in which Sorr1 acts as a transcriptional activator of the pathway, Sorr2 appears to act as an inhibitor of the Sorr1 activity. This would also explain why there are still low levels of sorbicillinoids

detected in the sorR2 deletion strain while these are completely ab-sent in the sorR2 overexpression strain in which the pathway is sup-pressed. This phenotype resembles that of the aflJ deletion strain of Aspergillus. aflJ and aflr are transcriptional factors that regulate the aflatoxin and sterigmatocystin cluster in Aspergillus parasiticus (Chang, 2003; yu and keller, 2005). Deletion of the individual genes abolished the production of these compounds. aflr is a transcriptional activa-tor. like the ΔsorR2 strain in our study, the aflatoxin structural genes

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103 DISCUSSIoN

in the aflJ deletion strain also remain expressed at low levels, and it has been suggested that alfJ forms an active complex with alfr, the main regulator of the pathway (Georgianna and Payne, 2009). Sum-marizing our results suggest that both transcriptional factors Sorr1 and Sorr2 orchestrate the biosynthesis of sorbicillinoids, with Sorr1 as main transcriptional activator and Sorr2 as a repressor of this bio-synthetic pathway (Figure 4B). a similar regulatory mechanism involv-ing two transcriptional factors, has been reported for the homologous cluster in T. reesei (Derntl et al., 2016).

a further observation is that mutational loss of sorbicillinoid pro-duction is accompanied by a dramatic repro-duction in the expression of the pathway genes. a possible explanation of this observation is that sorbicillinoids function as autoinducers. Indeed, when the strain defi-cient in sorbicillinoid production was fed with filtered medium of a sor-bicillinoid producing strain, a major upregulation of the sorbicillin gene cluster was noted (Figure 3). Neither the Δsorr1 nor the Δsorr2 mu-tants did show this sorbicillinoid-dependent transcriptional response. Interestingly, the transcriptional response of the core sorbicillin genes (sora, sorB, sorC) in the sorr2 deletion strain (Figure 3B) is similar to what is observed when strain DS68530 is fed with sorbicillinoids (Figure 3a). a possible scenario is that sorbicillinoids act on Sorr2, thereby relieving the inhibitory action of Sorr2 on the transcriptional activator Sorr1. In this respect, the expression of the sorbicillin clus-ter expression was partially rescued when the oEsorr2 strain was fed with sorbicillinoids (Figure 3D). also, overexpression of Sorr1 partially restored transcription, as according to our model, the higher levels of Sorr1 overcome the inhibitory effect of Sorr2 on transcription. We propose that Sorr2 interacts with Sorr1 to reduce its transcriptional activating activity, while sorbicillinoids relieve this inhibition by act-ing on Sorr2 (Figure 4B). This is one of the rare reported examples wherein the product of the synthesis pathway acts as an autoinducer of the expression of the pathway genes. The zearalenone (ZEa) bio-synthetic cluster gene of Fusarium graminearum, whose regulator iso-forms (ZEB2S and ZEB2l) are induced by its own toxin is another ex-ample of this phenomenon (Park et al., 2015).

In silico analysis indicates that the intergenic DNa region between sorB and sorA comprises three nucleotide binding motifs 5’CGGN(9) CGG, which may act as binding sites for Sorr1 to regulate the cluster.

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104 M echanism and r egula tion o f sorbicillin bios yn thesis b y Penicillium chry so genum DISCUSSIoN

Sorr1 belongs to the family of sequence-specific DNa- binding Zn2-Cys6 proteins. Such regulators appear to be present in approximately 90 % of the PkS encoding genes cluster in fungi ( Brakhage, 2012). In Aspergillus flavus, the deletion of the aflR gene that encodes for a Zn2-Cys6 type protein, abolished the expression of the aflatoxin and sterigmatocystin cluster, while the overexpression of the same gene increased the expression and production of these secondary metab-olites (yin and keller, 2011; Brakhage, 2012). Sorr1 appears to func-tion in a similar manner. addifunc-tionally, our results suggest that there is possible cross-talk between the sorbicillinoids gene cluster regula-tors (Sorr1 and Sorr2) and other biosynthetic pathways. When the sorR1 gene was deleted, enhanced production of compound [13] was observed, whereas in the Sorr1 overexpression strain, production of this compound was reduced. remarkably, this secondary metabolite is not related to sorbicillinoids and was also detected in the ΔsorA and ΔsorB strains in which sorbicillinoids biosynthesis is eliminated. Pos-sible crosstalk has been reported before in Aspergillus nidulans where the induction of the silent asperfuranone gene cluster was achieved through expression of the scpR gene that encodes a transcriptional regulator of the inp gene cluster (Bergmann et al., 2010; Fischer et al., 2016). however, we cannot exclude the possibility that the elevated levels of compound [13] is due to a greater availability of precursor molecules not used for sorbicillinoids biosynthesis.

In conclusion, our results support a model for sorbicillinoid produc-tion that includes the funcproduc-tions of the various gene products that are part of the sorbicillinoids gene cluster and an alternative branched path independently of SorC. additionally, it was demonstrated that the regulation of this pathway involves two transcriptional regulators while sorbicillinoids act as autoinducers of this pathway. This work opens possibilities to engineer the sorbicillinoids pathway for the effi-cient production of novel derivatives of pharmaceutical value.

Figure 4. Proposed model of the sorbicillin biosynthetic pathway and its

regu-lation. A) PKS domains in SorA and SorB are abbreviated as KS (ketosynthase), ACP (acyl carrier protein), KR (ketoreductase), DH (dehydratase), MT (methyl-transferase), ER (enoylreductase). Adapted from (Avramović, 2011; Fahad et al., 2014; Derntl et al., 2016; Salo et al., 2016). B) The auto-induction mechanism of

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CHAPTER 3 105 DISCUSSIoN Sorbicillinoids B) A) sorA sorB

sorR1 sorC sorR2 sorT sorD

sorR1

SorR1

Sorbicillin Biosynthesis Gene Cluster

? Precursor Acetylated KS S CH3 O ACP S COOH O Precursor Manolylated ACP S O O CH3 Triketide precursor ACP S O CH3 ACP S CH3 KR,DH,ER KR,DH ACP S O O O O CH3 Methylated hexaketide Cyclization and release O O CH3 H3C O CH3 O H O CH3 OH H3C HO CH3 Sorbicillin (1) 2'-3'Dihydrosorbicillin (2*) O CH3 OH H3C O H3C OH Sorbicillinol (3*) 2'-3'Dihydrosorbicillinol (4*) O CH3 OH H3C HO CH3 Sorbicillin (1) 2'-3'Dihydrosorbicillin (2) O CH3 OH H3C O H3C OH Sorbicillinol (3) 2'-3'Dihydrosorbicillinol (4) Path II Path I OH CH3 O H3C HO H3C OH Oxosorbicillinol (5,5*) O H3C OH CH3 HO H3C O H CH3 O CH3 HO HO CH3 OH ? SorA SorA SorB SorC SorD SorD Bisvertinolone O SorR2 CH3 CH3 O O +

pathway gene expression by sorbicillinoids which involves the two transcription factors SorR1 and SorR2. On top, a schematic representation of the gene clus-ter. Black solid arrows indicate a positive stimulation and the red arrows show a negative effect. Green arrows represent the promoters of the indicated genes.

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106 M echanism and r egula tion o f sorbicillin bios yn thesis b y Penicillium chry so genum CoNFlICT oF INTErEST CONFLICT OF INTEREST None declared. AUTHOR CONTRIBUTIONS

FGC designed the study, performed the experiments, wrote the man-uscript and carried out the data analysis. aJMD conceived the study, supervised and coordinated the design, the data interpretation and corrected the manuscript. yN participated in data analysis and helped to draft the manuscript. PPl and oS supported the mass spectrome-try and structural analysis and helped to draft the manuscript. ralB contributed in the coordination of the project and the revision of the manuscript

FUNDING

FGC was supported by Consejo Nacional de Ciencia y Tecnología (CoNaCyT, México) and Becas Complemento SEP (México). yN was supported by funding from the European Union’s Seventh Framework Programme FP7/207-2013, under grant agreement N° 607332. oS was funded by NWo | Stichting voor de Technische Wetenschappen (STW). ACKNOWLEDGMENTS

The authors acknowledge DSM Sinochem Pharmaceuticals (Delft, The Netherlands) for kindly providing the DS68530 strain.

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110 M echanism and r egula tion o f sorbicillin bios yn thesis b y Penicillium chry so genum SUPPorTING INForMaTIoN SUPPORTING INFORMATION

Table S1. Strains used in this study

Strain Genotype Source

DS68530 Penicillin Cluster free, Δku70, DSM Sinochem Pharmaceuticals Strains derived from DS68530:

DS68530Res13 AmdS marker, SorA (F146L) (Salo et al., 2016)

OEsorR1_68530 Phleo, pcbC::Pc21g05050 This study

OEsorR2_68530 Phleo, pcbC::Pc21g05090 This study

Strains derived from DS68530Res13:

ΔsorR1 Phleo, ΔPc21g05050 This study

ΔsorC Phleo, ΔPc21g05060 This study

ΔsorB Phleo, ΔPc21g05070 This study

ΔsorA Phleo, ΔPc21g05080 This study

ΔsorR2 Phleo, ΔPc21g05090 This study

ΔsorT Phleo, ΔPc21g05100 This study

ΔsorD Phleo, ΔPc21g05110 This study

OEsorR1 Phleo, pcbC::Pc21g05050 This study

OEsorR2 Phleo, pcbC::Pc21g05090 This study

Phleo, Phleomycin marker

Table S2. Primers used in this study.

Name Primer sequence (5’→3’) Reference

Cloning, gene inactivation

1 attB4F_sorR1 GGGGACAACTTTGTATAGAAAAGTTGGTATCAATGGGAT

GGAATTCCTGAGAGC This study

2 attB1R_sorR1 GGGGACTGCTTTTTTGTACAAACTTGGAAGTGTGCGAG

GGTTAGTCGATTGC This study

3 attB2F_sorR1 GGGGACAGCTTTCTTGTACAAAGTGGGCACGGATAGCA

ACTGAAGTGACGG This study

4 attB3R_sorR1 GGGGACAACTTTGTATAATAAAGTTGCGTCCTTCAAAGC

TTTACCAATGTGGC This study

5 attB4F_sorC GGGGACAACTTTGTATAGAAAAGTTGGCGAGTTCTTACG

CAAGC This study

6 attB1R_sorC GGGGACTGCTTTTTTGTACAAACTTGTGCTGGTATGGTAA

GCGAC This study

7 attB2F_sorC GGGGACAGCTTTCTTGTACAAAGTGGGTGGATTTGAGG

AATAACGAC This study

8 attB3R_sorC GGGGACAACTTTGTATAATAAAGTTGGAGACTGACTCCTC

CAAAGC This study

9 attB4F_sorB GGGGACAACTTTGTATAGAAAAGTTGGGCACCATACCAC

GGTATCC This study

10 attB1R_sorB GGGGACTGCTTTTTTGTACAAACTTGCAGCATATCTAACT

CATCACC This study

11 attB2F_sorB GGGGACAGCTTTCTTGTACAAAGTGGCGTCGGCCGTATT

GCCAGACTGC This study

12 attB3R_sorB GGGGACAACTTTGTATAATAAAGTTGGCCGCTGTTTCAC

CCGAGTAACC This study

13 attB4F_sorA GGGGACAACTTTGTATAGAAAAGTTGCGTCGGCCGTATT

GCCAGACTGC (Salo et al., 2016)

14 attB1R_sorA GGGGACTGCTTTTTTGTACAAACTTGGCCGCTGTTTCAC

CCGAGTAACC (Salo et al., 2016)

15 attB2F_sorA GGGGACAGCTTTCTTGTACAAAGTGGGGTCATGTCCGAG

AAGCTGTC (Salo et al., 2016)

16 attB3R_sorA GGGGACAACTTTGTATAATAAAGTTGCGCCCTTGTTGAA

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CHAPTER 3

111 SUPPorTING INForMaTIoN

Name Primer sequence (5’→3’) Reference

Cloning, gene inactivation

17 attB4F_sorR2 GGGGACAACTTTGTATAGAAAAGTTGCTTGTCCTTCTCT

GTAGTAGTAGCAGCAGC This study

18 attB1R_sorR2 GGGGACTGCTTTTTTGTACAAACTTGGTGTCAACCAATG

AAATAGCAGTCCGTC This study

19 attB2F_sorR2 GGGGACAGCTTTCTTGTACAAAGTGGGGACTTTGGAGAA

GGGTTGGTTTAGTGG This study

20 attB3R_sorR2 GGGGACAACTTTGTATAATAAAGTTGGGCACCTGGAACC

TGCACAACC This study

21 attB4F_sorT GGGGACAACTTTGTATAGAAAAGTTGGATGCATCTACCT

GAGGTCA This study

22 attB1R_sorT GGGGACTGCTTTTTTGTACAAACTTGCTGTATTGACTATG

GACAAGGC This study

23 attB2F_sorT GGGGACAGCTTTCTTGTACAAAGTGGCTGAGTGAGAGCT

GTTAGAAATG This study

24 attB3R_sorT GGGGACAACTTTGTATAATAAAGTTGATGACTGCCAAGT

CAAGAATAC This study

25 attB4F_sorD GGGGACAACTTTGTATAGAAAAGTTGGCGTCAGTTTACA

TGGCTAT This study

26 attB1R_sorD GGGGACTGCTTTTTTGTACAAACTTGGCCTGCATTTTGA

GATTG This study

27 attB2F_sorD GGGGACAGCTTTCTTGTACAAAGTGGTGAGCGAAGTTCT

GACTAGTG This study

28 attB3R_sorD GGGGACAACTTTGTATAATAAAGTTGGTACAGATGCAGA

GTTGACG This study

Cloning, overexpression

29 attB1F_Phleo GGGGACAAGTTTGTACAAAAAAGCAGGCTCCGTCGACT

ACATGTATCTGCATG This study

30 attB2R_Phleo GGGGACCACTTTGTACAAGAAAGCTGGGTCGCAAATTAA

AGCCTTCGAG This study

31 attB1F_pE+Phleo GGGGACAAGTTTGTACAAAAAAGCAGGCTCCTCTTGCG

TTACGGGCGTA This study

32 attB2R_Phleo+pIPNS GGGGACCACTTTGTACAAGAAAGCTGGGTCGGTGTCTAG

AAAAATAATGGTGAAA This study

33 Rv_Phleo+pIPNS CAGACCAATGCAGCAGGCCCAGTATAAGGAGCAAATTAA

AGCCTTCGAG This study

33 Fw_Phleo+pIPNS GTTTTGGGACGCTCGAAGGCTTTAATTTGCTCCTTATACT

GGGCCTGC This study

34 attB2F_OEsorR1 GGGGACAGCTTTCTTGTACAAAGTGGCCATGAGAAGGC

AACAGTCTGG This study

35 attB3R_OEsorR1 GGGGACAACTTTGTATAATAAAGTTGATCGGAAGACGTG

TGTTTATC This study

36 attB2F_OEsorR2 GGGGACAGCTTTCTTGTACAAAGTGGCCATGGAAAATGG

ATGCACTTC This study

37 attB3R_OEsorR3 GGGGACAACTTTGTATAATAAAGTTGATAGAAGAGCGAT

CACTCGAT This study

Southern blotting

38 KOsorR1_SB_F CGCATGTGAATTACGTTATG This study

39 KOsorR1_SB_R AGCTCTTCCGAGAAAGAGTC This study

40 KOsorC_SB_F GTTGAAGAGCTCTGGCAATAGT This study

41 KOsorC_SB_R GCTTGCGTAAGAACTCGC This study

42 KOsorB_SB_F GTACGGCAAATAGCTTCCA This study

43 KOsorB_SB_R TGGTAGACGCCTTCTGATC This study

44 KOsorA_SB_F CTACACATTACGGCTTGTACC This study

45 KOsorA_SB_R TGCAACTAGATGCATGTCTTC This study

46 KOsorR2_SB_R GAGTTGACACGTCTCATCG This study

47 KOsorR2_SB_R CTGGCATATCCAAGAATTCC This study

48 KOsorT_SB_F GTGCATGTTCTCCTTACAGACT This study

49 KOsorT_SB_R TGAAGCCAAGAGACAGGTC This study

50 KOsorD_SB_F CGTCAACTCTGCATCTGTAC This study

51 KOsorD_SB_R ATACTTCAAGCACAAGGCTC This study

52 OEsorR1_SB_F GATCCAAATCGACGATAGG This study

53 OEsorR1_SB_R ATCCAGTGCGGTACTTCAT This study

54 OEsorR2_SB_F GCCTTGTCCATAGTCAATACAG This study

55 OEsorR2_SB_R AATGAAGATCACGCAGACA This study

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112 M echanism and r egula tion o f sorbicillin bios yn thesis b y Penicillium chry so genum SUPPorTING INForMaTIoN

Name Primer sequence (5’→3’) Reference

Southern blotting

57 Cpcr _Phleo_R AATGGAAACGACCTGAGC This study

58 Cpcr _sorR1_F GCAGTAAGAGTGCACTGAAAC This study

60 Cpcr _sorR1_R CATTTATGAACGAGCCGAG This study

61 Cpcr _sorC_F GTATGCTGGAGATGCAAGAC This study

62 Cpcr _sorC_R CTAGATGCCTCACAACTCG This study

63 Cpcr _sorB_F GTGAGTACAAATGCGCCT This study

64 Cpcr _sorB_R ATGTGATACACGGTTCGC This study

65 Cpcr _sorA_F CGACTACTCAGGTCAAGAGTG This study

66 Cpcr _sorA_R AGTGTCTGATGCTGATGAATC This study

67 Cpcr _sorR2_F GACGCCATCAATCAATGT This study

68 Cpcr _sorR2_R GGACTCCGATGAGTTGAGT This study

69 Cpcr _sorT_F GCGAGACTAGTTCGATTCTG This study

70 Cpcr _sorT_R CTGCTTTAGTCTGAGCGCT This study

71 Cpcr _sorD_F GATGGCAAGATCTACGTGAG This study

72 Cpcr _sorD_R CTCAAGTGAATGACCGTAGC This study

Nucleobase indicated in bold reflect the attB sites for the recombination used by the Gateway Technology.

Phleo R ΔsorR1 5’F sorR1 3’F sorR1 sorR1 DS68530Res13 5’F sorR1 3’F sorR1 Eco32I Eco32I Eco32I Eco32I 3.5 kb 2.4 kb WM kb DS68530Res13ΔsorR1 23 9.4 6.6 4.4 2.3 2.0 Phleo R ΔsorC 5’F sorC 3’F sorC sorC 5’F sorC 3’F sorC Sal I Sal I Sal I Sal I 3.4 kb 2.5 kb Des68530Res13ΔsorC kb 23 9.4 6.6 4.4 2.3 2.0 WM 0.6 0.6 3.3 kb Phleo R ΔsorB 3’F sorB 5’F sorB sorB 3’F sorB 5’F sorB SpeI SpeI SpeI 8.3 kb 3.3 kb SpeI WM kb DS68530Res13ΔsorB 23 9.4 6.6 4.4 2.3 2.0 0.6 Phleo R ΔsorR2 5’F sorR2 3’F sorR2 sorR2 5’F sorR2 3’F sorR2 DraIII DraIII DraIII DraIII 3.3 kb 2.3 kb WM kb DS68530Res13ΔsorR2 23 9.4 6.6 4.4 2.3 2.0 0.6 DS68530Res13 Phleo R ΔsorT 5’F sorT 3’F sorT sorT 5’F sorT 3’F sorT ScaI ScaI ScaI ScaI 1.8 kb 2.8 kb WM kb ΔsorD 23 9.4 6.6 4.4 2.3 2.0 0.6 DS68530Res13 WM kb Δ sorT 23 9.4 6.6 4.4 2.3 2.0 0.6 DS68530Res13 Phleo R ΔsorD 5’F sorD 3’F sorD sorD 5’F sorD 3’F sorD NcoI SpeI NcoI SpeI 2.6 kb 5.0 kb SpeI NcoI SpeI OE_sorR1 5’F sorR1 3’F sorR1 sorR1 5’F sorR1 3’F sorR1 HindIII HindIII HindIII 6.7 kb WM kb DS68530Res13OE_sorR1 23 9.4 6.6 4.4 2.3 2.0 DS68530Res13 kb 23 9.4 6.6 4.4 2.3 2.0 WM 0.6 0.6 sorR1 pIPNS Phleo R HindIII 4.2 kb OE_sorR2 OE_sorR2 5’F sorR2 3’F sorR2 sorR2 5’F sorR2 3’F sorR2 HindIII HindIII HindIII 6.6 kb sorR2 pIPNS HindIII 4.1 kb Phleo R Phleo R ΔsorA 5’F sorA 3’F sorA sorA 5’F sorA 3’F sorA 2.3kb 8.2 kb WM kb DS68530Res13ΔsorA 23 9.4 6.6 4.4 2.3 2.0 0.6 SpeI SpeI SpeI SpeI DS68530Res13 DS68530Res13 DS68530Res13 DS68530Res13 DS68530Res13 DS68530Res13 DS68530Res13

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CHAPTER 3

113 SUPPorTING INForMaTIoN

Figure S1. Southern blot analysis of P. chrysogenum strains with

individ-ual sor gene deletions and sorR1 and sorR2 overexpression. gDNA from DS68530Res13 was used as a control. The restriction enzyme used to digest the gDNA and the expected fragment sizes are indicated.

Phleo R ΔsorR1 5’F sorR1 3’F sorR1 sorR1 DS68530Res13 5’F sorR1 3’F sorR1 Eco32I Eco32I Eco32I Eco32I 3.5 kb 2.4 kb WM kb DS68530Res13ΔsorR1 23 9.4 6.6 4.4 2.3 2.0 Phleo R ΔsorC 5’F sorC 3’F sorC sorC 5’F sorC 3’F sorC Sal I Sal I Sal I Sal I 3.4 kb 2.5 kb Des68530Res13ΔsorC kb 23 9.4 6.6 4.4 2.3 2.0 WM 0.6 0.6 3.3 kb Phleo R ΔsorB 3’F sorB 5’F sorB sorB 3’F sorB 5’F sorB SpeI SpeI SpeI 8.3 kb 3.3 kb SpeI WM kb DS68530Res13ΔsorB 23 9.4 6.6 4.4 2.3 2.0 0.6 Phleo R ΔsorR2 5’F sorR2 3’F sorR2 sorR2 5’F sorR2 3’F sorR2 DraIII DraIII DraIII DraIII 3.3 kb 2.3 kb WM kb DS68530Res13ΔsorR2 23 9.4 6.6 4.4 2.3 2.0 0.6 DS68530Res13 Phleo R ΔsorT 5’F sorT 3’F sorT sorT 5’F sorT 3’F sorT ScaI ScaI ScaI ScaI 1.8 kb 2.8 kb WM kb ΔsorD 23 9.4 6.6 4.4 2.3 2.0 0.6 DS68530Res13 WM kb Δ sorT 23 9.4 6.6 4.4 2.3 2.0 0.6 DS68530Res13 Phleo R ΔsorD 5’F sorD 3’F sorD sorD 5’F sorD 3’F sorD NcoI SpeI NcoI SpeI 2.6 kb 5.0 kb SpeI NcoI SpeI OE_sorR1 5’F sorR1 3’F sorR1 sorR1 5’F sorR1 3’F sorR1 HindIII HindIII HindIII 6.7 kb WM kb DS68530Res13OE_sorR1 23 9.4 6.6 4.4 2.3 2.0 DS68530Res13 kb 23 9.4 6.6 4.4 2.3 2.0 WM 0.6 0.6 sorR1 pIPNS Phleo R HindIII 4.2 kb OE_sorR2 OE_sorR2 5’F sorR2 3’F sorR2 sorR2 5’F sorR2 3’F sorR2 HindIII HindIII HindIII 6.6 kb sorR2 pIPNS HindIII 4.1 kb Phleo R Phleo R ΔsorA 5’F sorA 3’F sorA sorA 5’F sorA 3’F sorA 2.3kb 8.2 kb WM kb DS68530Res13ΔsorA 23 9.4 6.6 4.4 2.3 2.0 0.6 SpeI SpeI SpeI SpeI DS68530Res13 DS68530Res13 DS68530Res13 DS68530Res13 DS68530Res13 DS68530Res13 DS68530Res13

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