MptriA, an Acetyltransferase Gene Involved in Pigment

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Bioactive Constituents, Metabolites, and Functions

MptriA, an acetyltransferase gene involved in pigment biosynthesis in M. purpureus YY-1 Bin Liang, Xin-jun Du, Ping Li, Chanchan Sun, and Shuo Wang J. Agric. Food Chem., Just Accepted Manuscript • DOI: 10.1021/acs.jafc.8b00661 • Publication Date (Web): 10 Apr 2018 Downloaded from http://pubs.acs.org on April 11, 2018

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Journal of Agricultural and Food Chemistry

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Title:

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MptriA, an acetyltransferase gene involved in pigment biosynthesis in M.

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purpureus YY-1

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Authors:

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Bin Lianga, Xinjun Dua, Ping Lia, Chanchan Suna,Shuo Wang a, *

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Affiliation:

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a

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Technology), Ministry of Education, Tianjin 300457, China

Key Laboratory of Food Nutrition and Safety (Tianjin University of Science &

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* Corresponding Author:

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Shuo Wang

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Key Laboratory of Food Nutrition and Safety (Tianjin University of Science &

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Technology), Ministry of Education, Tianjin 300457, China

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Tel: 86-22-60912484

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Fax: 86-22-60912484

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E-mail: [email protected]

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ABSTRACT

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Monascus pigments (Mps) have been used as food colorants for several centuries in

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Asian countries. MptriA is a putative acetyltransferase gene involved in the MPs biosynthesis.

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In order to analyze the function of MptriA, an MptriA disruption strain (∆MptriA) and a

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complementation strain (∆MptriA::MptriA) were successfully obtained In addition to the loss

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of color, the disruption of MptriA had little effect on the phenotypes during growth on four

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different medium. The ∆MptriA strain showed decreased pigment and citrinin production

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during the liquid-fermentation process. Transcriptional analysis showed that the expression of

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several genes involved in the synthesis of pigments and citrinin was down-regulated in

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∆MptriA. These results demonstrated that the role of MptriA was to transfer an acyl group to

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the pyranoquinone structure of the polyketide chromophore during Monascus pigment

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biosynthesis and to influence the citrinin biosynthesis pathway. This study contributes to the

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exploration of pigment biosynthesis in M. purpureus.

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KEYWORDS: M. purpureus; MptriA gene; Pigments; Disruption; Complementation

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INTRODUCTION

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As significant traditional edible fungi, Monascus species have been used in food,

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medicine and industry for more than one thousand years, and more than one billion people

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consume Monascus-fermented products as part of their daily diet1, 2, 3. One of the most famous

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Monascus-fermented products, red fermented rice, has been used extensively as a natural food

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colorant, folk medicine, fermentation starter in East and Southeast Asia4, 5, 6, 7. Meanwhile,

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previous reports have shown that Monascus species can produce various natural and

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functional secondary metabolites, such as Monascus pigments (Mps), monacolin K, and

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γ-aminobutyric acid (GABA)8-10. Therefore, the utility of Monascus species has attracted the

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attention of many research teams.

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Among secondary metabolites of Monascus spp., pigments used as food additives for

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several centuries in Asian countries4, have been supposed as polyketides11, 12. Pigments

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produced by Monascus species can be divided into three major groups: red pigments

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(monascorubramine

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rubropunctatin), and yellow pigments (monascin and ankaflavin)13. To date, at least 90 kinds

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of Mps have been identified1, 14, and many showed multifarious biological activities such as

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preventing hypertension15, and lowering cholesterol16, hypolipidemic effects17, and

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anti-obesity18, 19, anti-tumor20, and anti-cancer activities21. Therefore, it is important to select a

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high pigment-producing strain using molecular biological methods and optimize the

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fermentation conditions to improve pigment production.

and

rubropunctamine),

orange

pigments

(monascorubrin

and

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Analysis of the genomes of M. pilosus, M. purpureus, and M. ruber via bioinformatics

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and RT-PCR showed that the Mps gene cluster contains a minimum of 16 genes, namely,

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MpigA (nonreducing polyketide synthase, NR-PKS), MpigB (transcription factor), MpigC

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(dehydrogenase), MpigD (3-O-transacetylase), MpigE (dehydrogenase), MpigF (monoamine

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oxidase), MpigG (oxidoreductase), MpigH (dehydrogenase), MpigI (transcription factor),

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MpigJ (fatty acid synthase, α subunit), MpigK (fatty acid synthase, β subunit), MpigL

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(ankyrin), MpigM (P450-monooxygenase), MpigN/O (monooxygenase), MpigP (unknown

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function), and MpigQ (transporter)3,

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themselves to studying the Mps biosynthesis pathway, several steps and the identities of

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related enzymes remain unclear or controversial1, 3. Mps biosynthesis is believed to follow a

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polyketide pathway, in which the PKS genes have been shown to be extremely important to

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the biosynthetic pathways of Mps, owning to targeted inactivation of MpPKS5 in M.

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purpureus or pksPT in M. ruber gave rise to loss of pigment24, 25. In addition to PKS, several

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genes involved in pigment biosynthesis have been investigated. Xie, et al.26 identified a

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pigment biosynthesis regulatory gene (pigR) in M. ruber M7, which upregulated pigment

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production. Targeted deletion of mrflbA, Mgb1 and Mgg1 resulted in phenotypic alterations

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such as decreased vegetative growth and asexual sporulation and altered citrinin and pigment

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production27, 28. Liu, et al.29 obtained an MpigE (as well as mppC in M. purpureus) gene

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deletion strain (∆MpigE), which yielded only four kinds of yellow pigment and very few red

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pigments but had no influence on citrinin. Liu, Zhou, Yi and Zhao23 reported that a mutant d

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in which an approximately 30-kb region of the pigment gene cluster from M. ruber M7 was

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deleted could induce the accumulation of high levels of M7PKS-1, which has been previously

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shown to be an initial intermediate of Mps. Balakrishnan, et al.30 discovered a reductase gene,

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mppE, that controls the biosynthesis of the yellow pigments, ankaflavin and monascin in the

22, 23

. Even though many researchers have devoted

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azaphilone polyketide pathway. Although many scientists3, 25, 31, 32 have contributed to the

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prediction of parts of the synthetic pathway of Mps, the identities of related genes involved in

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pigment biosynthesis remain unclear or controversial, which limits the practical industrial

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application of Monascus.

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In our previous studies3, transcriptional differences in M. purpureus YY-1 grown in

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different medium on the eighth day of growth indicated that MptriA is upregulated when M.

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purpureus is grown in rice medium (high-yield pigment states). Therefore, we predicted that

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the MptriA gene plays a very significant role in the production of pigments. Previous reports

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have shown that MptriA homologs are found in two relevant azaphilone biosynthetic gene

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clusters: azaD and cazE, which are involved in the biosynthesis of azanigerones and

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chaetoviridin, respectively33, 34. In this study, we constructed a putative acetyltransferase

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MptriA gene-deletion mutant of M. purpureus YY-1 and its revertant strain to investigate the

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role of MptriA, and the results revealed that ∆MptriA caused little phenotypic alterations in

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addition to colors and played a vital role in the production of some secondary metabolites,

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such as pigments and citrinin. This work will guide further exploration of the function of

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MptriA in the biosynthetic pathways of pigments in M. purpureus.

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MATERIALS AND METHODS

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Fungal strains, culture medium, and growth conditions. M. purpureus YY-1 obtained

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from Gutian Shenghua Monascus Ltd. of Ningde City (Fujian Province, China) was used for

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the generation of the ∆MptriA strain3. The ∆MptriA strain was used to generate the

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∆MptriA::MptriA strain. For phenotypic characterization, four kinds of medium were used,

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namely, potato dextrose agar medium (PDA), malt extract agar medium (MA), Czapek yeast

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extract agar medium (CYA), and glycerol nitrate agar medium (25%) (G25N)35. For

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sporulation, M. purpureus YY-1 was grown on COM medium (30 g of glucose, 3 g of peptone,

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0.5 g of KH2PO4, 0.5 g of MgSO4 per liter, pH 5.5-6.0). For total DNA extraction and to

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screen the constructed strains, MA medium supplemented with the appropriate antibiotic was

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used. All strains were maintained on MA slants at 28°C. Minimal medium (MM), induction

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medium

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tumefaciens-mediated transformation (ATMT)36. Luria-Bertani medium (LB), supplemented

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with antibiotic when necessary, was used to cultivate Escherichia coli for propagating

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plasmids. M. purpureus YY-1 and its derivatives and A. tumefaciens were grown at 28°C.

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Fungal spores and A. tumefaciens were co-cultured at 24°C for 3 days. E. coli DH5α was

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grown at 37°C for routine cloning. All strains and plasmids used in this study are listed in

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Table 1.

(IM)

and

co-cultivation

medium

(CM)

were

used

for

Agrobacterium

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DNA extraction. Fungal genomic DNA was isolated from mycelia grown on cellophane

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membranes covering MA plates using the cetyltrimethylammonium bromide (CTAB) method

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described by Shao, et al.37.

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Cloning and analysis of the MptriA gene. A pair of primers, MptriA-F/MptriA-R

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(Table 2), was designed to amplify the MptriA gene. PCR was carried out to amplify the

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MptriA gene from the genome of M. purpureus YY-13, and the protocol was as follows: initial

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denaturation at 94°C for 2 min; 30 amplification cycles of 98°C for 10 s, 55°C for 30 s, and

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68°C for 2.5 min; and a final extension step at 72°C for 10 min; a TProfessional thermal

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cycler (Biometra, Germany) was used for the PCR. The amino acid sequence encoded by

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MptriA

was

predicted

using

SoftBerry's

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FGENESH

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(http://linux1.softberry.com/berry.phtml), and the MptriA functional regions were analyzed

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using the Pfam 30.0 program (http://pfam.xfam.org/). The homology of the deduced amino

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acid sequence was analyzed using the BLASTP program on the NCBI web site

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(http://blast.ncbi.nlm.nih.gov/Blast.cgi).

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∆MptriA strain construction. To construct the MptriA disruption mutant, the 5′ and 3′

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flanking regions (2355 bp and 2297 bp, respectively) of the MptriA gene were amplified with

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the primer pairs triA5-F/triA5-R and triA3-F/triA3-R using KOD-FX DNA polymerase

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(Toyobo, Japan) (Table 2). The PCR products of the 5’ and 3’ flanking regions were purified

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and cloned into the pEASY-Blunt vector (Transgen, China) to generate pEBTL and pEBTR,

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respectively. Successful cloning of the inserts into the resulting plasmids was verified by

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sequencing. Then, pEBTL was digested with KpnI and ApaI and ligated into the

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corresponding sites of pAg1-H3 (a vector containing the hygromycin phosphotransferase

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gene hph) to generate pAgHL. Then, both pEBTR and pAgHL were digested with AscI and

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SbfI and ligated with T4 DNA ligase to generate the plasmid pAgHLR. A 2-kb SbfI-digested

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DNA fragment containing the neomycin phosphotransferase resistance gene (neo) from the

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plasmid pAgHN was inserted into the corresponding sites of pAgHLR, yielding pAgHNLR.

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The plasmid pAgHNLR was transformed into A. tumefaciens AGL-1 via ATMT as described

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previously38 with the exception that cellophane was used instead of nitrocellulose membrane

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during the co-culture phase. The A. tumefaciens AGL-1 clones containing pAgHNLR were

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incubated for transformation with M. purpureus YY-1 to yield the fungal transformants. All

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the fungal transformants were selected on MA plates supplemented with 200 µg/mL

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hygromycin B and 500 µg/mL cefotaxime. Hygromycin-resistant and neomycin-sensitive

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strains were selected, and ∆MptriA was confirmed by PCR analysis using the internal primers

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YtriA1-F/YtriA1-R, external the outer primers YtriA2-F/YtriA2-R and cross-validation

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primers YtriA3-F/YtriA3-R, and YtriA3-F/YtriA3-R (Table 2).

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Complementation of ∆MptriA with MptriA of M. purpureus YY-1. To further verify

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whether all the differences exhibited by the ∆MptriA strain were caused by the disruption of

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MptriA, this gene was complemented. For complementation, the entire MptriA gene along

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with a 760-bp upstream region containing the putative promoter region of the gene and a

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599-bp downstream region was amplified from wild-type M. purpureus YY-1 with the

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primers pair triA-F/triA-R and inserted into pEASY-Blunt to generate pEBtriA (Table 2).

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Successful cloning of the insert into the resulting plasmid was verified by sequencing. Then,

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the plasmids pEBtriA and pAgHN were digested with SacI and KpnI, and the 2727-bp DNA

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fragment containing the intact MptriA was inserted into the corresponding sites of pAgHN to

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generate pAgHNtriA. Finally, the plasmid pAgHNtriA was transformed into A. tumefaciens

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AGL-1; and then the A. tumefaciens AGL-1 clones containing pAgHNtriA were incubated for

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transformation with the ∆MptriA strain by ATMT, as described previously, to yield the

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MptriA-complementation strain (∆MptriA::MptriA) by ATMT as described previously38.

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Transformants were selected on MA plates supplemented with 20 µg/mL neomycin and 500

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µg/mL cefotaxime at 28ºC. Neomycin-resistant strains were selected. The complementation

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was confirmed by PCR amplification with the primer pairs YtriA1-F/YtriA1-R and

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Neo-F/Neo-R (Table 2).

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Southern hybridization analysis. To further verify the homologous recombination

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events, Southern hybridization analysis was conducted. For Southern blot assays, the DIG

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High Prime DNA Labeling and Detection Starter Kit II (Roche, Germany) was used

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according to the manufacturer’s protocol. The DNA (20 µg) of the M. purpureus YY-1,

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putative ∆MptriA and ∆MptriA::MptriA strains were digested with XhoI. Probe 1 and probe 2

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were amplified via PCR with the primer pairs ProtriA-F/ProtriA-R and Prohph-F/Prohph-R

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(Table 2), respectively. Probe 1 and probe 2 were used to verify the MptriA disruptant, and the

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∆MptriA::MptriA strain was confirmed with probe 1.

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RNA isolation and complementary DNA preparation. Total RNA of M. purpureus

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YY-1, ∆MptriA, and ∆MptriA::MptriA was isolated from mycelia after 48 h of cultivation

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using the RNeasy® Plant Mini Kit (QIAGEN, Germany) according to the manufacturer’s

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protocol. RNA concentration was determined by measuring the absorbance at 260 and 280 nm

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(A260/A280), and RNA integrity was verified by visualization on 1% agarose gels. RNA

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samples were stored at −80°C. For reverse transcription, total RNA (390 ng) was added to a

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20 µL mixture derived from the PrimeScript™ RT Reagent Kit (Takara, Japan), and the

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reaction conditions followed the manufacturer’s protocol.

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Quantitative real-time PCR analysis. The changes in mRNA levels obtained by

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RNA-seq were further validated by quantitative real-time PCR (qRT-PCR) of the MptriA gene.

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Each reaction (20 µL) contained 10 µL of SYBR Premix Ex Taq II, 0.8 µL of 10 µM forward

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primer, 0.8 µL of 10 µM reverse primer, 0.4 µL of ROX Reference Dye II (Takara, Japan), 2

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µL of template cDNA, and 6 µL of ddH2O. All real-time PCRs were performed using the

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Mastercycler ep realplex system (Eppendorf, Germany) with the following steps (two-step

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PCR amplification, standard procedure): 30 s at 95°C, 40 cycles of 5 s at 95°C, and 34 s at

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60°C. Sample melting curves were assessed to evaluate the specificity of the amplification.

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GAPDH was used as the reference gene29. The primers used in this part are listed in Table 2.

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Samples were analyzed in triplicate, and the experiments were repeated at least three times.

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MP and Citrinin analysis. Three kinds of COM medium (100 mL) with appropriate

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antibiotics were fermented by the wild-type strain M. purpureus YY-1, ∆MptriA or

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∆MptriA::MptriA. After agitation with 170 rpm for 40 h at 30°C, 20 mL of the fermentation

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mixtures of the above three strains were inoculated into 200 mL of RM medium (20 g of rice

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powder, 20 g of glucose, 20 g of peptone, 2 g of NaNO3, 1.5 g of KH2PO4, 1 g of MgSO4 per

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liter) with the appropriate antibiotics. The fermentation was carried out at 28ºC, and samples

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were taken every other day from the 2nd day to the 18th day of fermentation to measure MP

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and citrinin production. In addition, samples were harvested from 2 d to 8 d for RNA isolation

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and transcriptional analysis by real-time PCR.

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MP production was detected by following the method described by the Chinese

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standards (GB 1816.15-2015) with slight modification. The supernatant was removed by

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centrifugation from the fermentation broth, and the fungal mycelia were washed twice with

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sterile water and then dried at 60°C in a hot air oven until a constant weight was attained.

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Dried mycelia (0.02 g) were treated with 10 mL of 70% ethanol and heated at 60°C in water

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for 1 h. After filtration, the absorbance values of the red, orange, and yellow pigments were

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determined at the specific wavelengths 505 nm, 465 nm and 410 nm, respectively, using a 50

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Bio UV-Visible spectrophotometer (Cary Varian, USA); 70% ethanol was used as a negative

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control. Pigment yield was expressed as absorbance at the λmax of the pigment per g of dry M.

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purpureus YY-1 mycelia39.

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To detect citrinin production, HPLC was performed following the method described by

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the Chinese standards (GB/T 5009.222-2008) with slight modification. After filtration and

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drying as described above, 0.01 g of dried mycelia was extracted with 1 mL of

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acetate/formic acid (TEF, 7:3:1 by volume) buffer. The prepared samples were filtered

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through a 0.2-µm filter and analyzed by HPLC using a reverse-phase C18 column (5 µm, 4.6

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mm×250 mm). The HPLC parameters were as follows: mobile phase, 75% (v/v)

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acetonitrile/25% (v/v) water (pH 2.5, adjusted by orthophosphoric acid); column temperature,

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28°C; flow rate, 1.0 mL/min. The elution was monitored using a fluorescence detector at an

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emission wavelength of 500 nm and an excitation wavelength of 331 nm. A citrinin standard

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(Sigma, USA) was used to verify the HPLC analysis.

toluene/ethyl

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Transcriptome sequencing and analysis. Vegetative hyphae of M.purpureus YY-1 and

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∆MptriA were harvested from 8-d liquid RM cultures. There were three biological replicates

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for each strain. Transcriptome sequencing and analysis were performed by Novogene

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Bioinformatics Technology Co., Ltd. (Beijing, China). Briefly, Total RNA was extracted using

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TRIzol reagent according to the manufacturer’s protocol. RNA purity was checked using a

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NanoPhotometer® spectrophotometer (Implen, USA). RNA concentration and integrity were

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measured using the Qubit® RNA Assay Kit with a Qubit® 2.0 Fluorometer (Life Technologies,

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USA) and the RNA Nano 6000 Assay Kit with a Bioanalyzer 2100 system (Agilent

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Technologies, USA). Then, mRNA was purified from total RNA using poly-T oligo-attached

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magnetic beads, and fragmentation was carried out using NEBNext First Strand Synthesis

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Reaction Buffer. The obtained mRNA fragments were used as templates to synthesize

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first-strand cDNA with random hexamer primers, and then, the second-strand cDNA was

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synthesized using DNA polymerase I and RNase H. After adenylation of the 3’ ends of the

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DNA fragments, NEBNext Adaptor was ligated to prepare the samples for hybridization.

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cDNA that were 150-200 bp in length were preferentially size-selected and purified with the

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AMPure XP system (Beckman Coulter, USA). After PCR amplification, the library

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preparations were sequenced on an Illumina HiseqTM 2000 sequencer (Illumina, USA), and

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125 bp/150-bp paired-end reads were generated. The index of the reference genome was built

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using Bowtie v2.2.3, and paired-end clean reads were aligned to the reference genome using

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TopHat v2.0.12. Gene expression was calculated using the FPKM (expected fragments per kb

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of transcript per million mapped reads) method with HTSeq v0.6.1, and differentially

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expressed genes were selected based on P-value