Genomic characteristics and comparative genomics analysis of Penicillium chrysogenum KF-25
- Qin Peng†1,
- Yihui Yuan†1,
- Meiying Gao1Email author,
- Xupeng Chen1, 2,
- Biao Liu1,
- Pengming Liu1,
- Yan Wu1 and
- Dandan Wu1
© Peng et al.; licensee BioMed Central Ltd. 2014
Received: 31 July 2013
Accepted: 6 February 2014
Published: 21 February 2014
Penicillium chrysogenum has been used in producing penicillin and derived β-lactam antibiotics for many years. Although the genome of the mutant strain P. chrysogenum Wisconsin 54-1255 has already been sequenced, the versatility and genetic diversity of this species still needs to be intensively studied. In this study, the genome of the wild-type P. chrysogenum strain KF-25, which has high activity against Ustilaginoidea virens, was sequenced and characterized.
The genome of KF-25 was about 29.9 Mb in size and contained 9,804 putative open reading frames (orfs). Thirteen genes were predicted to encode two-component system proteins, of which six were putatively involved in osmolarity adaption. There were 33 putative secondary metabolism pathways and numerous genes that were essential in metabolite biosynthesis. Several P. chrysogenum virus untranslated region sequences were found in the KF-25 genome, suggesting that there might be a relationship between the virus and P. chrysogenum in evolution. Comparative genome analysis showed that the genomes of KF-25 and Wisconsin 54-1255 were highly similar, except that KF-25 was 2.3 Mb smaller. Three hundred and fifty-five KF-25 specific genes were found and the biological functions of the proteins encoded by these genes were mainly unknown (232, representing 65%), except for some orfs encoding proteins with predicted functions in transport, metabolism, and signal transduction. Numerous KF-25-specific genes were found to be associated with the pathogenicity and virulence of the strains, which were identical to those of wild-type P. chrysogenum NRRL 1951.
Genome sequencing and comparative analysis are helpful in further understanding the biology, evolution, and environment adaption of P. chrysogenum, and provide a new tool for identifying further functional metabolites.
The filamentous fungus Penicillium chrysogenum has been widely used for producing penicillin and derived β-lactam antibiotics for more than 80 years. The discovery of penicillin has greatly improved human health and promoted the development of the medical industry. In addition to producing penicillin, P. chrysogenum has exhibited abilities in others areas, including bioleaching, biological remediation, promoting plant growth, and producing non-β-lactam antibiotics and antifungal agents[2–6]. According to previous reports, several P. chrysogenum strains produce secreted proteins, such as PAF, PgAFP, and PgChP, which inhibit the growth of opportunistic zoopathogens, plant-pathogenic fungi, and toxigenic molds[7–9]. With their high stability, effective inhibitory activity, and broad inhibition spectra, these three proteins could be effective antifungal agents in medicine and agriculture[10, 11].
In 2008, van den Berg et al. reported the first sequence of the P. chrysogenum genome and genes that were responsible for key steps in penicillin production were identified. The genome not only led to a deeper understanding of penicillin synthesis, but also provided a new tool for identifying additional metabolites. The sequenced P. chrysogenum strain Wisconsin 54-1255 was a model laboratory strain that was derived from wild-type NRRL 1951, which was isolated from infected cantaloupe[14, 15]. As a mutant strain used in the laboratory, Wisconsin 54-1255 might be some genetic variations, such as reduced PahA activity, encoded by pahA, in the catabolism of phenylacetic acid (the side chain precursor for the synthesis of benzylpenicillin). Moreover, different P. chrysogenum isolates maintain diverse genetic backgrounds[17, 18], and studying the genome sequences of other strains will providemore information on the genetic diversity of P. chrysogenum. Therefore, sequencing the genome of a wild-type P. chrysogenum strain is necessary.
P. chrysogenum KF-25 is a wild-type strain isolated from a soil sample by our laboratory. It shows high-anti-fungal activity against Ustilaginoidea virens, which causes false smut disease of rice and corn in humid areas, in contrast to the Wisconsin 54-1255 strain, which did not exhibit anti-fungal activity. This suggested that there might be differences in the genetic backgrounds of the two strains. To provide more genetic information on P. chrysogenum to identify additional active substances and to determine the critical genes involved in the biosynthesis of the active substances, we sequenced and analyzed the genome of KF-25. Comparative genome analysis of strain KF-25 with Wisconsin 54-1255 and the wild-type strain NRRL 1951 revealed significant genetic variance. We also analyzed the functions and distribution of the genes encoding several important proteins, including transporters, non-ribosomal peptide synthase, and two-component regulatory systems (TCRSs).
Results and discussion
Genome sequence and annotation of P. chrysogenum KF-25
General genome features
General genome features of P. chrysogenum KF-25 and P. chrysogenum Wisconsin 54-1255
P. chrysogenum KF-25
P. chrysogenum Wisconsin 54-1255 []
Assembly sizes (Mb)
GC content (%)
Mean gene length (bp)
Exons per gene
Introns per gene
In total, 317 repetitive elements were found in the genome of strain KF-25 by RepeatScout, with a minimum length 50 bp and a maximum length of 1,296 bp. Repetitive sequence analysis by using CENSOR indicated that 648,249 bp of the KF-25 genome (2.17%) was repeat sequences, while the repeat content of Wisconsin 54-1255 was 1.04%.
Microsatellites (simple sequence repeats, SSRs) are one of the most popular genetic markers and exist widely in fungal genomes. Because of high mutation rate and changing in repeat numbers during DNA replication, SSRs exhibit high individual specificity[20–22]. In the genome of KF-25, 3,798 SSRs were found, with sizes ranging from 15to 167 bp, and these SSRs were homogenously distributed throughout the genome (Additional file1: Figure S1).
The secretory system and transporter
Translocation of protein and molecule across the plasma membrane is essential for cell life and requires the help of secretory systems and transporters, such as signal recognition particle (SRP) and the Sec translocase[23, 24]. SRP plays a critical role in targeting of secretory proteins to the cellular membrane, while the Sec secretion system is responsible for protein translocation across the cytoplasmic membrane. P. chrysogenum has been widely used to produce penicillin and some other secondary metabolites with antimicrobial activity[2, 7–9, 27, 28]. The secretory system and transporters are essential for secretion of these antimicrobial substances and for import of their substrates. In the KF-25 genome, 12 proteins were predicted to be components of the eukaryotic Sec-SRP secretion systems (Additional file1: Table S4). These proteins might play important roles in protein secretion in P. chrysogenum. Several genes in the genome of KF-25 encoded transporters or components of the secretion system that involved in producing penicillin and other secondary metabolites. KF-25 genome contained 531 genes that encoded transporter proteins, which mainly belonged to the major facilitator superfamily (MFS, 231 genes), and the ABC transporter superfamily (52 genes). Several genes in the secondary metabolism gene cluster were predicted to encode MFS-type transporters by antiSMASH. The MFS transporters in the penicillin synthesis pathway could regulate the production of penicillin and enhance the sensitivity of P. chrysogenum to phenylacetic acid. Many ABC superfamily transporters in the KF-25 genome were predicted to be multidrug resistance proteins. One ABC superfamily transporter was reported to be critical in the export of phenylacetic acid, which is the precursor of penicillin synthesis. There were also several other transporters in the KF-25 genome that are involved in sugar, amino acid, cation, and vitamin transport.
Two-component regulatory system
The genes encoding the proteins involving in the two-component systems in the genome of P. chrysogenum KF-25 and corresponding genes in the genome of P. chrysogenum Wisconsin 54-1255
Genes in Genome of KF-25
Putative protein function
Corresponding genes in P. chrysogenum Wisconsisn 54-1255
osmolarity two-component system, response regulator SSK1
Pc20g02430 (98% identify)
two-component system, NarL family, capsular synthesis sensor histidine kinase RcsC
Pc22g18780 (99% identify)
osmolarity two-component system, response regulator SKN7
Pc22g04440 (99% identify)
two-component system, chemotaxis family, sensor kinase Cph1
Pc06g00040 (99% identify)
two-component system, unclassified family, sensor histidine kinase and response regulator
Pc16g03520 (99% identify)
two-component system, cell cycle sensor kinase and response regulator
Pc12g07950 (96% identify)
two-component system, NarL family, capsular synthesis sensor histidine kinase RcsC
Pc22g07510 (99% identify)
osmolarity two-component system, phosphorelay intermediate protein YPD1
Pc22g12510 (100% identify)
osmolarity two-component system, response regulator SSK1
Pc22g16340 (99% identify)
osmolarity two-component system, response regulator SSK1
Pc13g13580 (88% identify)
osmolarity two-component system, response regulator SSK1
Pc13g13880 (99% identify)
two-component system, unclassified family, sensor histidine kinase and response regulator
Pc13g09080 (99% identify)
two-component system, unclassified family, sensor histidine kinase and response regulator
Pc20g15550 (99% identify)
Comparative genomics and phylogenetic analysis of P. chrysogenum KF-25
Comparative genome analysis of P. chrysogenum KF-25 and P. chrysogenum Wisconsin 54-1255
Comparative analysis of P. chrysogenum KF-25 and other P. chrysogenum strains
According to previous proteomic studies, the improvement process of penicillin production enhanced the expression of some genes, while decreasing[15, 41, 42]. P. chrysogenum Wisconsin 54-1255 is a moderately improved penicillin producer derived from the wild-type P. chrysogenum NRRL 1951, which exhibited more secondary metabolism pathways (such as pigments), pathogenicity proteins and virulence proteins compared with Wisconsin 54-1255 and another high penicillin producer P. chrysogenum AS-P-78[15, 42]. P. chrysogenum KF-25 is a wild-type strain that had a stronger yellow pigment production than Wisconsin 54-1255 (Figure 1). The ability to produce more pigments is representative of a greater number of secondary metabolic pathways, and was a common feature of both KF-25 and NRRL 1951. Several KF-25-specific genes were found to be associated with pathogenicity and virulence. One such gene, KF25_6369, which encodes glucose oxidase, is thought to be involved in virulence because gluconic acid and glucose oxidase are related to pathogenicity of Penicillium espansum in apples. Glucose oxidase also showed reduced expression in Wisconsin 54-1255, compared with NRRL 1951. The penicillin synthesis genes were clustered in one group in the genomes of NRRL 1951 and Wisconsin 54-1255, while several such clusters were found in the AS-P-78 genome. Similar to wild-type NRRL 1951, KF-25 contained only one penicillin synthesis gene cluster. Wild-type P. chrysogenum KF-25 and NRRL 1951 have more secondary metabolism pathways and more pathogenicity and virulence associated genes, which are fitness mechanisms for the wild-type strains to survive in natural environment.
Phylogenetic analysis of P. chrysogenum KF-25 and the other sequenced filamentous fungi
Secondary metabolism analysis of P. chrysogenum KF-25
Putative secondary metabolism pathways
P. chrysogenum has been known as a penicillin producer for many years. Recently, studies have mainly focused on the pathways of penicillin synthesis, and the key genes involving involved in penicillin production have been determined[13, 27, 46]. In additional to penicillin, P. chrysogenum can produce many other secondary metabolites, such as mycotoxin and drugs[27, 28, 47, 48]. In a previous report, SMURF analysis predicted that the genome of Wisconsin 54-1255 contains 33 secondary metabolism gene clusters. In this study, secondary metabolism gene clusters was predicted using antiSMASH, and 33 and 41 gene clusters were identified in the genomes of KF-25 and Wisconsin 54-1255 (Additional file1: Table S7 and Figure S6). The predicted products of 23 secondary metabolism gene clusters in KF-25 were: eight nonribosomal peptides, 10 polyketides, two hybrid non-ribosomal peptide synthase (NRPS)-polyketide synthases (PKS), one hybrid NRPS-terpene, one terpene and one siderophore, while the remainding 10 gene clusters produced other secondary metabolites (Additional file1: Table S7). Among the 33 gene clusters, five were predicted to produce stigmatellin, chalcomycin, epothilone, fumitremorgin and penicillin. The production of penicillin by KF-25 and Wisconsin 54-1255 were verified by HPLC (Additional file1: Figure S7). The data showed that Wisconsin 54-1255 exhibited greater ability of producing penicillin than KF-25.
Non-ribosomal peptide synthetase
NRPSs play important roles in the synthesis of non-ribosomal peptides, which include antibiotics and other important pharmaceuticals. In the P. chrysogenum KF-25 genome, 20 NRPS genes were found and the domain compositions of these predicted NRPSs are shown in Additional file1: Figure S8. Among the 20 predicted NRPSs, 14 were involved in putative secondary metabolism pathways, while the other six were not. Eleven of the 20 predicted NRPSs, encoded by gene KF25_6155, KF25_1342, KF25_6525, KF25_1526, KF25_9456, KF25_5703, KF25_8966, KF25_6509, KF25_8398, KF25_9347, and KF25_4993, had similar amino acid sequences to HC-toxin synthase. In addition, 15 of the predicted MFS transporters encoded by the KF-25 genome were identified as HC-toxin efflux carriers. The HC-toxins determine the specificity and virulence of pathogenic fungi toward host plants. The existence of the HC-toxin synthases and HC-toxin efflux carriers suggested that P. chrysogenum KF-25 might produce HC-toxin.
Cytochrome P450s (CYPs) are hemoproteins that are ubiquitously distributed throughout all domains of life and play important and diverse roles in metabolic processes and adaptation to different environmental niches by fungi. CYPs participating in numerous primary, secondary, and xenobiotic metabolic reactions have been reported[61, 62], and several CYPs predicted from sequenced microorganism genomes were found to be members of secondary metabolism pathways[63, 64]. CYPs can be classified into different families based on the amino acid sequences[65, 66]. Ninety CYPs were predicted in the KF-25 genome (about 0.9% of total ORFs) and many of them were members of putative secondary metabolism pathways, including the pathways of PKSs, NRPSs, andNRPS-terpenes. These CYPs belonged to 60 different families. There were usually one or two CYPs per family but some families contained three to six CYPs (Figure 6b). The classifications of the CYPs from the Wisconsin 54-1255 genome were almost the same as those from KF-25 genome (Additional file1: Figure S9). As a multicomponent electron transport chain system, CYPs are critical in degradation, detoxification, and syntheses of life-critical compounds in organisms. Besides their functions in secondary metabolism, CYPs also play critical roles in the adaption of organisms to specific ecological niches and the biosynthesis of physiologically important compounds[68, 69]. The existence of so many CYPs might be essential for the life cycle P. chrysogenum and the synthesis of the metabolic products, such as penicillin.
P. chrysogenum virus terminal fragment-similar sequences
In this study, we reported the genome sequence of wild-type P. chrysogenum KF-25. This is the second report of a P. chrysogenum genome, but the first of wild-type strain. Comparative genome analysis showed that KF-25 genome lacked regions of the genome, totaling 2.3 Mb, that were found in Wisconsin 54-1255 genome, which were previously considered to be P. chrysogenum species-specific regions. However, our results showed that the missing regions were only specific to Wisconsin 54-1255. These regions contained numerous repeat elements and transposable elements, indicating that these segments might have been obtained by Wisconsin 54-1255 through transposition and horizontal gene transfer during evolution. Comparative analysis of KF-25 with another wild-type strain, NRRL 1951, revealed that they had numerous features in common, such as pigments production, and a greater number of pathogenicity- and virulence-associated genes. Based on the phylogenetic tree of 90 conserved orthologous proteins, strains KF-25 and Wisconsin 54-1255 maintained a close evolutionary distance. Analysis of the TCRSs indicated that many proteins were osmolarity TCRSs, which may be an adaptive strategy of P. chrysogenum to high osmotic pressure. Several gene clusters involved in putative secondary metabolism pathways, and many genes encoding essential enzymes for the biosynthesis of diverse biologically-active agents were found, which could provide foundation for using P. chrysogenum to produce antibiotics including penicillin and other β-lactam antibiotics. The identification of P. chrysogenum virus UTR sequences in the two sequenced P. chrysogenum genomes is helpful for studying the relationship between the virus and its fungal host in evolution. The results of this study can help us to further understand the genetic diversity of P. chrysogenum and shed light on its evolution, biology, environmental adaption and application.
Strains and culture conditions
P. chrysogenum strain KF-25 and U. virens strain UV-1 were isolated and identified by our lab. Strain Wisconsin 54-1255 was provided by MA van den Berg at DSM Anti-Infectives. Fungal strains were grown in potato-sucrose (PS) medium [20% (w/v) potato lixivium, 2% (w/v) sucrose], and 1.5% (w/v) agar was used in solid potato-sucrose medium (PSA). To assay the antifungal activity, P. chrysogenum strains KF-25 and Wisconsin 54-1255 were grown in 500-ml flasks containing 100 ml of PS medium at 28°C for 96 h with shaking (180 rpm). The culture supernatants were filtered through four layers of cheesecloth and centrifugated at 16000 × g for 20 min at 4°C. The culture supernatants were sterilized by filtering through a 0.22 μm membrane (Millipore) and were used to assay the antifungal activity against U. virens using the disk diffusion test. The conidia of pathogen U. virens were spread on a PSA plate at a density of 108 spores/ml and 100 μl spore suspension was used for each plate, then 20 μl of the sterilized culture supernatant above was added to a piece of sterile filter paper with a 6 mm diameter, placed in the center of the plate. The plate was incubated for 5 days at 28°C. Assays were performed in triplicate.
Conidiospores of P. chrysogenum KF-25 and Wisconsin 54-1255 were inoculated at 105 to 106 conidia/ml in a production medium containing (g/l): glucose · H2O, 5; lactose · H2O, 80; (NH2)2CO, 4.5; (NH4)2SO4, 1.1; Na2SO4, 2.9; KH2PO4, 5.2; K2HPO4 · 3H2O ,4.8; trace elements solution (citric acid · H2O, 150; FeSO4 · 7H2O,15; MgSO4 · 7H2O, 150; H3BO3,0.0075; CuSO4 · 5H2O, 0.24; CoSO4 · 7H2O, 0.375; ZnSO4 · 7H2O, 1.5; MnSO4 · H2O, 2.28; CaCl2 · 2H2O, 0.99), 10 (ml/l); 10% phenylacetic acid, pH 7, 75 (ml/l) and the pH was adjusted to pH 6.5 before inoculation. The culture was incubated at 25°C in an orbital shaker at 280 rpm for 4 days. The mycelium was removed by centrifugation and filtration, and the fermentation broth was assayed for penicillin by HPLC-DAD (High Performance Liquid Chromatography-Diode Array Detector). The assay was performed on a Dionex UltiMate 3000 RS HPLC system with autosampler and a DAD detector (Thermo Fisher Scientific, Waltham, MA) and an Agilent ZORBAX 300SB-C18 column (250 × 4.6 mm, 5 μm particle size, Agilent Technologies, Palo Alto, CA). The mobile phase was consisted of solvents A [0.5 mol/L KH2PO4 (pH3.5): methanol: water, 1:3:6] and B [0.5 mol/L KH2PO4 (pH3.5): methanol: water, 1:5:4]. The gradient program started with 30% of B, followed by increasing to 100% B from 0 to 20 min, held at 100% B from 20 to 35 min, decreasing to 30% of B from 35 to 50 min. The flow rate was 1.0 ml/min with a column temperature of 25°C. The injection volume was 20 μl, and the detection wavelength was 210 nm. Penicillin G (0.5 mg/ml) was used as a positive control.
The cultures of P. chrysogenum KF-25 and Wisconsin 54-1255 in potato-sucrose (PS) medium for 4 days were analysed by HPLC on a Dionex UltiMate 3000 RS HPLC system with autosampler and a DAD detector and a Sepax Polar-Silica column (250 × 10.0 mm, 5 μm particle size, Sepax Technologies, Newark, DE). The mobile phase consisted of solvents A (10 mM ammonium acetate) and B (methanol). The program held at 80% B from 0 to 20 min. The flow rate was 2.0 ml/min and the column temperature was 25°C. The injection volume was 5 μl, and the detection wavelength was 210 nm.
Genome sequencing, assembly, and annotation
Whole-genome sequencing of KF-25 was performed by the National Center for Gene Research, Shanghai, China. KF-25 genomic DNA was extracted as described previously, then was randomly sheared and purifiedto construct three libraries with insert sizes of 170 bp, 500 bp and 2–3 kb. DNA was amplified from the libraries and sequenced by HiSeq2000 (Illumina, California, USA). The reads were assembled into contigs by Velvet (Version 1.2.03) and then scaffolds were constructed based on the contigs using SSPACE.
AUGUSTUSugustus (http://bioinf.uni-greifswald.de/augustus/) was used to predict the genes in the KF-25 genome, and the putative proteins were aligned against the NCBI nr, UniProt (http://www.uniprot.org/) and KEGG (http://www.genome.jp/kegg/) database using BLASTP tool (http://blast.ncbi.nlm.nih.gov/Blast.cgi). The predicted genes were then aligned against the CDD database (http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi) using rpsBLAST. To identify the KOG classification of each gene, we searched for each amino acid sequence in the KOG database in NCBI using KOGnitor (http://www.ncbi.nlm.nih.gov/COG/grace/kognitor.html). Metabolic pathways of the KF-25 genome were constructed based on the annotation results against the KEGG database. Repeat sequences were analyzed using CENSOR (http://www.girinst.org/censor/index.php). The genes encoding tRNA were predicted using tRNAScan, and RNAmmer was used to find rDNA sequences. P. chrysogenum virus terminal UTR sequences in the KF-25 genome were identified using local BLAST and the sequences were aligned using ClustalX 2.0.
Comparative genome analysis
Mauve software was used to compare the genome of KF-25 with Wisconsin 54-1255 [GenBank:NS_000201.1]. Dot plot analysis of the two genomes was performed with Gepard. The orthologous genes between KF-25 and Wisconsin54-1255 were by compared the proteomes of the two genomes and proteins that exhibited similarity higher than 25% were thought orthologous. Proteins encoded by all of the strain-specific genes were classified by searching the eukaryotic orthologous groups (KOG) database in NCBI using KOGnitor.
Detection of strain-specific genes from P. chrysogenum
The genomic DNA of KF-25 and Wisconsin 54-1255 was extracted as described previously. Four pairs of primers based on specific gene sequences of Wisconsin 54-1255 (Additional file1: Table S8) were used to amplify specific genes by PCR (primers used were listed in Additional file1: Table S8). The products were detected on an agarose gel.
Secondary metabolism-related gene analysis
The secondary metabolism pathways in the KF-25 and Wisconsin 54-1255 genomes were predicted using antiSMASH (http://antismash.secondarymetabolites.org/). Modular polyketide synthases in the genome were predicted and the domain compositions were analyzed using AMSPKS and Pfam. Genome-encoded cytochrome P450s were classified by searching against the fungal cytochrome P450 database.
Phylogenetic trees were constructed in MEGA 5.05, using the neighbor-joining method and bootstrap analysis (1,000 replicates), of MUSCLE or ClustalW alignments. Phylogenetic trees of filamentous fungi were constructed as described previously using the aligned amino acid sequences of 90 orthologous genes from P. chrysogenum KF-25, P. chrysogenum Wisconsin 54-1255 [GenBank:NS_000201.1], P. marneffei [GenBank:ABAR00000000], P. digitatum, T. stipitatus [GenBank:ABAS00000000], A. niger, A. nidulans [GenBank:AACD00000000], A. oryzae, Aspergillus fumigatus, Aspergillus clavatus [GenBank:AAKD00000000], Aspergillus terreus [GenBank:AAJN00000000], Aspergillus flavus [GenBank:AAIH00000000], Aspergillus kawachii, Neosartorya fischeri [GenBank:AAKE00000000], and Gibberella zeae [GenBank:AACM00000000] (Additional file1: Table S9).
The complete genome sequence of P. chrysogenum KF-25 has been submitted to SRA (http://www.ncbi.nlm.nih.gov/sra/) under the accession number SRP022930.
We thank van den Berg MA at DSM Anti-Infectives for providing Penicillium chrysogenum Wisconsin 54-1255. This study was supported by the National Natural Science Foundation of China (No.31170123, 31201560), the National Project (2009ZX08009-056B), and the projects of the Chinese Academy of Sciences (KSCX2-EW-G-16).
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