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Applied and Environmental Microbiology, August 2007, p. 5097-5103, Vol. 73, No. 16
0099-2240/07/$08.00+0 doi:10.1128/AEM.01979-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.
,
Hiroshi Kinoshita,1 and
Takuya Nihira1,2*
International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan,1 MU-OU Collaborative Research Center for Bioscience and Biotechnology, Faculty of Science, Mahidol University, Rama VI Rd., 10400 Bangkok, Thailand2
Received 21 August 2006/ Accepted 9 June 2007
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Regulators possessing a Zn(II)2Cys6 binuclear motif represent one of the largest classes of transcriptional regulators in filamentous fungi. They generally act as transcriptional activators, as exemplified by GAL4 from Saccharomyces cerevisiae (21). A large number of Zn(II)2Cys6 regulators have been identified exclusively in fungi and characterized as regulators of primary metabolism, secondary metabolism, drug resistance, or meiotic development. Through its DNA binding motif (CX2CX6CX6CX2CX6C [C, cysteinyl residue; X, any amino acid]) located at the N terminus, the Zn(II)2Cys6 regulator binds to a specific binding site (CGGN6/11CCG [N, any nucleotide]) in the promoter regions of target genes. Previous research on secondary metabolites in filamentous fungi revealed that several gene clusters contain this type of activator gene and that the activator plays a major role in synchronizing the expression of several genes in the biosynthetic cluster (22).
The mycotoxin citrinin (CT) was first isolated as a secondary metabolite from Penicillium citrinum (12) and was subsequently identified in many fungal species, such as Penicillium, Aspergillus, and Monascus. CT was first considered an antibiotic against gram-positive bacteria, but toxicity studies have revealed that it should be regarded as a mycotoxin, based on its nephrotoxicity to humans, causing endemic Balkan nephropathy (16).
The fungus Monascus purpureus is highly useful for its ability to produce red pigments (11) as a food colorant,
-aminobutyric acid as an antihypertensive agent, and monacolin K as an antihypercholesterolemic agent. However, its potential for producing CT limits its wider use. Detailed knowledge of the biosynthetic pathway and regulation mechanism is required to eliminate possible contamination by CT in food products. In our previous study, a polyketide synthase (PKS) gene for CT (pksCT) was cloned from M. purpureus (18). In this study, we cloned the genes in the vicinity of pksCT to obtain new genes involved in CT biosynthesis. An activator gene essential for the efficient production of CT was found in the upstream region of pksCT, and we demonstrate that an extremely low-CT producer can be created by disrupting the gene.
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For the genetic manipulation of Escherichia coli, E. coli XL10-Gold ultracompetent cells (Stratagene, La Jolla, CA) and Library Efficiency DB3.1 competent cells (Invitrogen, Carlsbad, CA) were used as the cloning hosts.
Southern and Northern blot analyses.
Southern and Northern blot analyses were conducted essentially by the method of Sambrook et al. (17). For Southern blot analysis, genomic DNA (20 µg) was digested overnight with restriction enzyme, separated on a 1.0% agarose gel, and transferred to a Hybond N+ membrane (Amersham Biosciences, Piscataway, NJ). For Northern blot analysis, total RNA (8 µg) was separated on a 1% agarose-formaldehyde gel. The probe was labeled with [
-32P]dCTP using the Random Primer DNA labeling kit, version 2 (Takara Bio, Otsu, Japan).
Colony hybridization.
To clone the CT biosynthetic gene cluster, four successive rounds of Southern blot analysis were conducted with four different probes. Probes A, B, C and D were the 1.6-kb EcoRI (I)-SacI (I) fragment, the 960-bp XbaI (I)-EcoRI (II) fragment, the 750-bp EcoRI (III)-EcoRV fragment, and the 820-bp SalI-SacI (II) fragment, respectively, and they hybridized to a 2.7-kb HindIII (I)-XbaI (I) fragment, a 2.6-kb EcoRI (I)-EcoRI (II) fragment, a 5.0-kb XbaI (I)-XbaI (II) fragment, and a 4.1-kb SalI-HindIII (II) fragment, respectively (Fig. 1). (The Roman numbers in parentheses indicate the specific site among several sites for the corresponding restriction enzyme.) Monascus genomic DNA was digested with each restriction enzyme and electrophoresed on a 1% agarose gel. Corresponding regions were extracted and subcloned into the multicloning site of pUC19, resulting in the construction of individual partial genomic libraries. From each library, 2,000 colonies were selected. Positive clones were then identified by colony hybridization with each probe.
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FIG. 1. Restriction enzyme map of cloned fragments. The 5.0-kb XbaI (I)-XbaI (II), 4.1-kb SalI-HindIII (II), 2.6-kb EcoRI (I)-EcoRI (II), and 2.7-kb HindIII (I)-XbaI (I) fragments were obtained by colony hybridization. orf1, orf2, orf3, orf4, and orf5 indicate identified genes encoding a homolog of a dehydrogenase, a regulator, an oxygenase, an oxidoreductase, and a transporter, respectively. pksCT is the CT PKS gene. The thick black arrows indicate position and direction. Probes A, B, C, and D are the 1.6-kb EcoRI (I)-SacI (I), 960-bp XbaI (I)-EcoRI (II), 750-bp EcoRI (III)-EcoRV, and 820-bp SalI-SacI (II) regions, respectively.
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RT-PCR.
For reverse transcriptase PCR (RT-PCR), total RNA was extracted from Monascus mycelia cultivated in MC liquid medium every other day from the second to the sixth day of cultivation using the RNeasy Mini Kit (QIAGEN, Tokyo, Japan), according to the manufacturer's protocol, and treated with DNase I to remove the contaminating genomic DNA. The cDNA was synthesized with SuperScript III RNase H– RT (Invitrogen). For PCR, the amplification conditions were 25 cycles of denaturation (95°C for 30 s), annealing (55°C for 30 s), and extension (72°C for 2 min), followed by a single extension at 72°C for 4 min. The primers used in this study are shown in Table 1.
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TABLE 1. Primers used in this study
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FIG. 4. orf2 disruption by double crossover via homologous recombination (A) and PCR (left) and Southern blot (right) analyses of the orf2 disruptant (B). The orf2 gene was disrupted by inserting the hygromycin resistance gene (open arrow, Hygr) from pReg-dis (see Materials and Methods). The small arrows indicate the primers, dis F and dis R, used for PCR analysis. A part of the hygromycin resistance gene was used as a probe for Southern blot analysis (the double-headed arrow under Hygr). W, wild-type strain; D, ctnA disruptant.
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Analysis of pigment and CT production.
Monascus was cultivated in MC liquid medium as described above. The amounts of CT and pigment in the mycelia and in the mycelium-free filtrate were measured every other day from the second to the tenth day of cultivation, as described by Shimizu et al. (18, 19). The mycelia harvested by suction-filtration were dried in an oven at 80°C for 3 days.
Nucleotide sequence accession number.
The sequence surrounding the pksCT gene determined in this study has been deposited in the DDBJ database under accession number AB243687.
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TABLE 2. Sequence analysis of putative ORFs
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FIG. 2. Transcriptional analysis of putative CT biosynthetic genes. (A) RT-PCR was performed against RNA samples extracted from mycelia harvested from MC liquid medium after the indicated period of cultivation. (B) Northern blot analysis of the pksCT gene. Shown is the fragment amplified by RT-PCR, with the primers pksCT F and pksCT R used as a probe. W, wild-type strain; D, ctnA disruptant; E, ctnA-complemented ctnA disruptant; act (encoding actin), control.
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FIG. 3. Structure of ctnA. In the sequences of the 5' and 3' termini of ctnA, arrows mark the TSS and termination site. The underlined sequence is a putative polyadenylation site. The thick black arrow indicates the ctnA gene, of 2,006 bp, encoding a 576-amino-acid protein with four introns shown by empty rectangles (with intron sizes shown). The rectangle on the far left indicates the position of the Zn(II)2Cys6 DNA binding motif. The large, bold letters in the highlighted sequence are cysteinyl residues constituting the Zn(II)2Cys6 DNA binding motif at the N terminus.
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The orf2 disruptant did not show any significant differences from the wild-type strain in either growth (Fig. 5A) or pigment production (Fig. 5B). However, in sharp contrast to the progressive production of CT by the wild-type strain (1,930 µg per flask at 10 days' cultivation), CT production in the orf2 disruptant was kept very low (less than 0.1 µg per flask) throughout the cultivation period (Fig. 5C), suggesting that the orf2 product is important for the efficient production of CT. Regarding PksCT, a central player in CT biosynthesis as the PKS for CT, RT-PCR revealed a drastic reduction in its transcription in the orf2 disruptant (Fig. 2A). Northern blot analysis confirmed that pksCT transcription was almost negligible in the orf2 disruptant (Fig. 2B), indicating that the orf2 product is necessary for transcriptional activation of pksCT. In addition to pksCT, RT-PCR also suggested that the orf2 product would be required for the efficient transcription of orf5, though the weak effect was observed for orf3 transcription. These results suggested that, as in the case of AflR in the aflatoxin biosynthetic cluster (9), the orf2 product (designated CtnA for being the first factor related to CT biosynthesis other than PksCT) acts as an activator at least on pksCT and orf5 transcription. This occurs probably through binding to specific DNA sequences in the upstream region of each of the two genes, although no definite conserved sequence was discovered in the promoter regions of pksCT and orf5.
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FIG. 5. Phenotypic analysis of the ctnA disruptant and the ctnA-complemented ctnA disruptant. (A) Growth in liquid culture. Growth was expressed by the weight of dry mycelia for the wild-type strain (diamonds), the ctnA disruptant (squares), and the ctnA-complemented ctnA disruptant (triangles). (B) Pigment production. Pigments were extracted from dry mycelia with 70% ethanol, and the optical density at 500 nm (OD500) was measured for the wild-type strain (diamonds) and the ctnA disruptant (squares). (C) Comparison of CT production among the wild-type strain (diamonds), the ctnA disruptant (squares), and the ctnA-complemented ctnA disruptant (triangles). The CT contents in both the mycelia and mycelium-free filtrate were measured by high-performance liquid chromatography and enzyme-linked immunosorbent assay, and the sum is shown. These experiments were performed at least three times independently.
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FIG. 6. Complementation of the ctnA disruptant by intact ctnA, as determined by Southern blot analysis of the ctnA-complemented strain. Part of the regulator gene was used as a probe (see the double-headed arrow above ctnA in Fig. S1 of the supplemental material). By BglI digestion, any strains containing ctnA show a 1.3-kb band (corresponding to fragment B1-B2 in Fig. S1 in the supplemental material). By SalI digestion, any strains containing pAG-reg-derived ctnA show a 2.2-kb band (fragment S0-S2 in Fig. S1 in the supplemental material), while the wild-type strain shows a 3.0-kb band (fragment S1-S2 in Fig. S1 in the supplemental material). The band smaller than 2.2 kbp in strains E1 and E2 may indicate the presence of genome-integrated pAG-reg in addition to the autonomously existing pAG-reg. E4 was selected for phenotypic analysis. P, pAG-reg (positive control); W, wild-type strain; E1 to E4, ctnA-complemented ctnA disruptants; D, ctnA disruptant.
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In this study, we investigated the presence of the genes involved in CT production in the flanking regions of pksCT and discovered five putative ORFs (orf1, ctnA, orf3, and orf4 in the 5'-flanking region and orf5 in the 3'-flanking region of pksCT). A database search revealed the plausible functions of the encoded proteins as a dehydrogenase for orf1, a transcriptional activator for orf2 (ctnA), an oxygenase for orf3, an oxidoreductase for orf4, and a transporter for orf5 (Table 2). The presence of an oxygenase (orf3) and an oxidoreductase (orf4) corresponds well to the proposed pathway of CT biosynthesis (10), which, together with their positions adjacent to pksCT, raises the possibility that ctnA, orf3, orf4, pksCT, and orf5 may be involved in CT biosynthesis. Based on BLASTP alignments, the product of ctnA was found to be most similar (27% identity and 38% similarity) to a transcriptional regulator for pisatin demethylase (AY218847) from Nectria haematococca, which contains a Zn(II)2Cys6 DNA binding motif (14). Based on the results that (i) ctnA disruption drastically decreased CT production (to 0.0016% of that of the wild-type strain) and (ii) the disruptant regained CT production by the complementation of intact ctnA, ctnA is predicted to be a required factor for efficient CT production. Transcriptional analysis of the ctnA disruptant revealed that ctnA disruption affected the transcription of pksCT and orf5, though the effect on orf3 was not clear. Again, complementation of the intact ctnA restored the transcription of pksCT and orf5 to wild-type levels. These findings, taken together with the recovery of CT production, suggest that the ctnA gene encodes a transcriptional activator for the CT biosynthetic cluster, including pksCT. In the ctnA-complemented strain, however, cellular growth did not reach the wild-type level throughout cultivation and the production of CT was higher from the second to the sixth day and lower from the eighth to the tenth day than in the wild-type strain. This might be attributed to the uncontrolled expression of ctnA under the constitutive trpC promoter, which could result in the production of CT to levels harmful to cellular growth in the early phase of cultivation.
Zn(II)2Cys6-type regulators have been reported to activate target genes by binding to consensus binding sequences consisting of conserved terminal trinucleotides (CGGN6CCG or CGGN11CCG) in their promoter regions (21). Searches for such conserved sequences revealed none in the promoter region of either pksCT or orf5, whose transcripts were dramatically decreased in the ctnA disruptant. Therefore, different terminal trinucleotides might be recognized by CtnA. In the future, in vitro analysis using recombinant CtnA, such as a gel shift assay or DNase I footprinting, will clarify the actual CtnA binding site in the CT biosynthetic cluster.
CT was first discovered in Penicillium citrinum (12) and was considered an antibiotic, but it was later clarified to be a nephrotoxin to animals, including humans (16). Subsequent research discovered that several species of Penicillium, Aspergillus (15), and Monascus (5) produce CT. Moreover, CT contamination has been detected in wheat, oats, rye, corn, barley, and rice in many countries (4). This paper is the first report of the presence of an activator of CT biosynthesis among CT-producing fungi. The identification of an activator and an apparent CT biosynthetic gene cluster in Monascus may aid in the identification of corresponding gene clusters in different fungal species and in the development of strategies for suppressing CT production through the application of detailed knowledge of the regulation of CT biosynthesis.
This paper is part of the Ph.D. dissertation of T.S.
Published ahead of print on 22 June 2007. ![]()
Supplemental material for this article may be found at http://aem.asm.org/. ![]()
Present address: Department of Life Sciences, Faculty of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan. ![]()
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