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Liu X, Wang X, Zhou F, Xue Y, Liu C. Genomic insights into Penicillium chrysogenum adaptation to subseafloor sedimentary environments. BMC Genomics 2024; 25:4. [PMID: 38166640 PMCID: PMC10759354 DOI: 10.1186/s12864-023-09921-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 12/17/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Penicillium chrysogenum is a filamentous fungal species with diverse habitats, yet little is known about its genetics in adapting to extreme subseafloor sedimental environments. RESULTS Here, we report the discovery of P. chrysogenum strain 28R-6-F01, isolated from deep coal-bearing sediments 2306 m beneath the seafloor. This strain possesses exceptional characteristics, including the ability to thrive in extreme conditions such as high temperature (45 °C), high pressure (35 Mpa), and anaerobic environments, and exhibits broad-spectrum antimicrobial activity, producing the antibiotic penicillin at a concentration of 358 μg/mL. Genome sequencing and assembly revealed a genome size of 33.19 Mb with a GC content of 48.84%, containing 6959 coding genes. Comparative analysis with eight terrestrial strains identified 88 unique genes primarily associated with penicillin and aflatoxins biosynthesis, carbohydrate degradation, viral resistance, and three secondary metabolism gene clusters. Furthermore, significant expansions in gene families related to DNA repair were observed, likely linked to the strain's adaptation to its environmental niche. CONCLUSIONS Our findings provide insights into the genomic and biological characteristics of P. chrysogenum adaptation to extreme anaerobic subseafloor sedimentary environments, such as high temperature and pressure.
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Affiliation(s)
- Xuan Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, China
| | - Xinran Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, China
| | - Fan Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, China
| | - Yarong Xue
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, China
| | - Changhong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, China.
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Wang W, Zhang B, Zhang M, Zhang Z, Wang Y, Ge X, DU Y, Zhang X, Liu X, Wang J, Wang X, Shi S. [Mining and identification of a biosynthetic gene cluster producing xanthocillin analogues from Penicillium chrysogenum MT-40, an endophytic fungus of Huperzia serrata]. Sheng Wu Gong Cheng Xue Bao 2023; 39:3814-3826. [PMID: 37805856 DOI: 10.13345/j.cjb.221035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 10/09/2023]
Abstract
Xanthocillin is a unique natural product with an isonitrile group and shows remarkable antibacterial activity. In this study, the genome of an endophytic fungus Penicillium chrysogenum MT-40 isolated from Huperzia serrata was sequenced, and the gene clusters with the potential to synthesize xanthocillin analogues were mined by local BLAST and various bioinformatics analysis tools. As a result, a biosynthetic gene cluster (named for) responsible for the biosynthesis of xanthocillin analogues was identified by further heterologous expression of the key genes in Aspergillus oryzae NSAR1. Specifically, the ForB catalyzes the synthesis of 2-formamido-3-(4-hydroxyphenyl) acrylic acid, and the ForG catalyzes the dimerization of 2-formamido-3-(4-hydroxyphenyl) acrylic acid to produce the xanthocillin analogue N, N'-(1, 4-bis (4-hydroxyphenyl) buta-1, 3-diene-2, 3-diyl) diformamide. The results reported here provide a reference for further discovery of xanthocillin analogues from fungi.
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Affiliation(s)
- Wenjing Wang
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Beibei Zhang
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Mingliang Zhang
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Zekun Zhang
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Yang Wang
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Xiangyu Ge
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Yu DU
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Xiaoxue Zhang
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Xiao Liu
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Juan Wang
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Xiaohui Wang
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Shepo Shi
- Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
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Zhgun AA, Eldarov MA. Polyamines Upregulate Cephalosporin C Production and Expression of β-Lactam Biosynthetic Genes in High-Yielding Acremonium chrysogenum Strain. Molecules 2021; 26:molecules26216636. [PMID: 34771045 PMCID: PMC8588317 DOI: 10.3390/molecules26216636] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 10/28/2021] [Accepted: 10/30/2021] [Indexed: 12/18/2022] Open
Abstract
The high-yielding production of pharmaceutically significant secondary metabolites in filamentous fungi is obtained by random mutagenesis; such changes may be associated with shifts in the metabolism of polyamines. We have previously shown that, in the Acremonium chrysogenum cephalosporin C high-yielding strain (HY), the content of endogenous polyamines increased by four- to five-fold. Other studies have shown that the addition of exogenous polyamines can increase the production of target secondary metabolites in highly active fungal producers, in particular, increase the biosynthesis of β-lactams in the Penicillium chrysogenum Wis 54-1255 strain, an improved producer of penicillin G. In the current study, we demonstrate that the introduction of exogenous polyamines, such as spermidine or 1,3-diaminopropane, to A. chrysogenum wild-type (WT) and HY strains, leads to an increase in colony germination and morphological changes in a complete agar medium. The addition of 5 mM polyamines during fermentation increases the production of cephalosporin C in the A. chrysogenum HY strain by 15-20% and upregulates genes belonging to the beta-lactam biosynthetic cluster. The data obtained indicate the intersection of the metabolisms of polyamines and beta-lactams in A. chrysogenum and are important for the construction of improved producers of secondary metabolites in filamentous fungi.
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Tóth L, Boros É, Poór P, Ördög A, Kele Z, Váradi G, Holzknecht J, Bratschun‐Khan D, Nagy I, Tóth GK, Rákhely G, Marx F, Galgóczy L. The potential use of the Penicillium chrysogenum antifungal protein PAF, the designed variant PAF opt and its γ-core peptide Pγ opt in plant protection. Microb Biotechnol 2020; 13:1403-1414. [PMID: 32207883 PMCID: PMC7415367 DOI: 10.1111/1751-7915.13559] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/28/2020] [Accepted: 03/02/2020] [Indexed: 12/14/2022] Open
Abstract
The prevention of enormous crop losses caused by pesticide-resistant fungi is a serious challenge in agriculture. Application of alternative fungicides, such as antifungal proteins and peptides, provides a promising basis to overcome this problem; however, their direct use in fields suffers limitations, such as high cost of production, low stability, narrow antifungal spectrum and toxicity on plant or mammalian cells. Recently, we demonstrated that a Penicillium chrysogenum-based expression system provides a feasible tool for economic production of P. chrysogenum antifungal protein (PAF) and a rational designed variant (PAFopt ), in which the evolutionary conserved γ-core motif was modified to increase antifungal activity. In the present study, we report for the first time that γ-core modulation influences the antifungal spectrum and efficacy of PAF against important plant pathogenic ascomycetes, and the synthetic γ-core peptide Pγopt , a derivative of PAFopt , is antifungal active against these pathogens in vitro. Finally, we proved the protective potential of PAF against Botrytis cinerea infection in tomato plant leaves. The lack of any toxic effects on mammalian cells and plant seedlings, as well as the high tolerance to harsh environmental conditions and proteolytic degradation further strengthen our concept for applicability of these proteins and peptide in agriculture.
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Affiliation(s)
- Liliána Tóth
- Institute of Plant BiologyBiological Research CentreTemesvári krt. 62H‐6726SzegedHungary
| | - Éva Boros
- Institute of BiochemistryBiological Research CentreTemesvári krt. 62H‐6726SzegedHungary
| | - Péter Poór
- Department of Plant BiologyFaculty of Science and InformaticsUniversity of SzegedKözép fasor 52H‐6726SzegedHungary
| | - Attila Ördög
- Department of Plant BiologyFaculty of Science and InformaticsUniversity of SzegedKözép fasor 52H‐6726SzegedHungary
| | - Zoltán Kele
- Department of Medical ChemistryFaculty of MedicineUniversity of SzegedDóm tér 8H‐6720SzegedHungary
| | - Györgyi Váradi
- Department of Medical ChemistryFaculty of MedicineUniversity of SzegedDóm tér 8H‐6720SzegedHungary
| | - Jeanett Holzknecht
- Institute of Molecular BiologyBiocenterMedical University of InnsbruckInnrain 80‐82A‐6020InnsbruckAustria
| | - Doris Bratschun‐Khan
- Institute of Molecular BiologyBiocenterMedical University of InnsbruckInnrain 80‐82A‐6020InnsbruckAustria
| | - István Nagy
- Institute of BiochemistryBiological Research CentreTemesvári krt. 62H‐6726SzegedHungary
| | - Gábor K. Tóth
- Department of Medical ChemistryFaculty of MedicineUniversity of SzegedDóm tér 8H‐6720SzegedHungary
- MTA‐SZTE Biomimetic Systems Research GroupUniversity of SzegedDóm tér 8H‐6720SzegedHungary
| | - Gábor Rákhely
- Department of BiotechnologyFaculty of Science and InformaticsUniversity of SzegedKözép fasor 52H‐6726SzegedHungary
- Institute of BiophysicsBiological Research CentreTemesvári krt. 62H‐6726SzegedHungary
| | - Florentine Marx
- Institute of Molecular BiologyBiocenterMedical University of InnsbruckInnrain 80‐82A‐6020InnsbruckAustria
| | - László Galgóczy
- Institute of Plant BiologyBiological Research CentreTemesvári krt. 62H‐6726SzegedHungary
- Department of BiotechnologyFaculty of Science and InformaticsUniversity of SzegedKözép fasor 52H‐6726SzegedHungary
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5
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Ding Z, Zhou H, Wang X, Huang H, Wang H, Zhang R, Wang Z, Han J. Deletion of the Histone Deacetylase HdaA in Endophytic Fungus Penicillium chrysogenum Fes1701 Induces the Complex Response of Multiple Bioactive Secondary Metabolite Production and Relevant Gene Cluster Expression. Molecules 2020; 25:molecules25163657. [PMID: 32796640 PMCID: PMC7464707 DOI: 10.3390/molecules25163657] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/08/2020] [Accepted: 08/09/2020] [Indexed: 12/04/2022] Open
Abstract
Epigenetic regulation plays a critical role in controlling fungal secondary metabolism. Here, we report the pleiotropic effects of the epigenetic regulator HdaA (histone deacetylase) on secondary metabolite production and the associated biosynthetic gene clusters (BGCs) expression in the plant endophytic fungus Penicillium chrysogenum Fes1701. Deletion of the hdaA gene in strain Fes1701 induced a significant change of the secondary metabolite profile with the emergence of the bioactive indole alkaloid meleagrin. Simultaneously, more meleagrin/roquefortine-related compounds and less chrysogine were synthesized in the ΔhdaA strain. Transcriptional analysis of relevant gene clusters in ΔhdaA and wild strains indicated that disruption of hdaA had different effects on the expression levels of two BGCs: the meleagrin/roquefortine BGC was upregulated, while the chrysogine BGC was downregulated. Interestingly, transcriptional analysis demonstrated that different functional genes in the same BGC had different responses to the disruption of hdaA. Thereinto, the roqO gene, which encodes a key catalyzing enzyme in meleagrin biosynthesis, showed the highest upregulation in the ΔhdaA strain (84.8-fold). To our knowledge, this is the first report of the upregulation of HdaA inactivation on meleagrin/roquefortine alkaloid production in the endophytic fungus P. chrysogenum. Our results suggest that genetic manipulation based on the epigenetic regulator HdaA is an important strategy for regulating the productions of secondary metabolites and expanding bioactive natural product resources in endophytic fungi.
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Affiliation(s)
- Zhuang Ding
- Institute of BioPharmaceutical Research, Liaocheng University, Liaocheng 252059, China; (X.W.); (R.Z.); (Z.W.); (J.H.)
- Correspondence: ; Tel./Fax: +86-635-8239136
| | - Haibo Zhou
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China;
| | - Xiao Wang
- Institute of BioPharmaceutical Research, Liaocheng University, Liaocheng 252059, China; (X.W.); (R.Z.); (Z.W.); (J.H.)
| | - Huiming Huang
- School of Life Science, Liaocheng University, Liaocheng 252059, China;
| | - Haotian Wang
- Faculty of Pharmacy, Bengbu Medical College, Bengbu 233000, China;
| | - Ruiyan Zhang
- Institute of BioPharmaceutical Research, Liaocheng University, Liaocheng 252059, China; (X.W.); (R.Z.); (Z.W.); (J.H.)
| | - Zhengping Wang
- Institute of BioPharmaceutical Research, Liaocheng University, Liaocheng 252059, China; (X.W.); (R.Z.); (Z.W.); (J.H.)
| | - Jun Han
- Institute of BioPharmaceutical Research, Liaocheng University, Liaocheng 252059, China; (X.W.); (R.Z.); (Z.W.); (J.H.)
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García-Estrada C, Martín JF, Cueto L, Barreiro C. Omics Approaches Applied to Penicillium chrysogenum and Penicillin Production: Revealing the Secrets of Improved Productivity. Genes (Basel) 2020; 11:genes11060712. [PMID: 32604893 PMCID: PMC7348727 DOI: 10.3390/genes11060712] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/07/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022] Open
Abstract
Penicillin biosynthesis by Penicillium chrysogenum is one of the best-characterized biological processes from the genetic, molecular, biochemical, and subcellular points of view. Several omics studies have been carried out in this filamentous fungus during the last decade, which have contributed to gathering a deep knowledge about the molecular mechanisms underlying improved productivity in industrial strains. The information provided by these studies is extremely useful for enhancing the production of penicillin or other bioactive secondary metabolites by means of Biotechnology or Synthetic Biology.
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Affiliation(s)
- Carlos García-Estrada
- INBIOTEC (Instituto de Biotecnología de León). Avda. Real 1—Parque Científico de León, 24006 León, Spain; (L.C.); (C.B.)
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
- Correspondence: or ; Tel.: +34-987210308
| | - Juan F. Martín
- Área de Microbiología, Departamento de Biología Molecular, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain;
| | - Laura Cueto
- INBIOTEC (Instituto de Biotecnología de León). Avda. Real 1—Parque Científico de León, 24006 León, Spain; (L.C.); (C.B.)
| | - Carlos Barreiro
- INBIOTEC (Instituto de Biotecnología de León). Avda. Real 1—Parque Científico de León, 24006 León, Spain; (L.C.); (C.B.)
- Departamento de Biología Molecular, Universidad de León, Campus de Ponferrada, Avda. Astorga s/n, 24401 Ponferrada, Spain
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Martín JF. Insight into the Genome of Diverse Penicillium chrysogenum Strains: Specific Genes, Cluster Duplications and DNA Fragment Translocations. Int J Mol Sci 2020; 21:ijms21113936. [PMID: 32486280 PMCID: PMC7312703 DOI: 10.3390/ijms21113936] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/19/2020] [Accepted: 05/29/2020] [Indexed: 11/24/2022] Open
Abstract
Background: There are eighteen species within the Penicillium genus section chrysogena, including the original penicillin producers Penicillium notatum (Fleming strain) and Penicillium chrysogenum NRRL 1951. Other wild type isolates of the Penicillium genus are relevant for the production of useful proteins and primary or secondary metabolites. The aim of this article is to characterize strain specific genes and those genes which are involved in secondary metabolite biosynthesis, particularly the mutations that have been introduced during the β-lactams strain improvement programs. Results: The available genomes of several classical and novel P. chrysogenum strains have been compared. The first genome sequenced was that of the reference strain P. chrysogenum Wis54-1255, which derives from the wild type P. chrysogenum NRRL 1951; its genome size is 32.19 Mb and it encodes 12,943 proteins. Four chromosomes were resolved in P. chrysogenum and P. notatum by pulse field gel electrophoresis. The genomes of three industrial strains have a similar size but contain gene duplications and truncations; the penicillin gene cluster copy number ranges from one in the wild type to twelve in the P. chrysogenum ASP-E1 industrial strain and is organized in head to tail tandem repeats. The genomes of two new strains, P. chrysogenum KF-25, a producer of antifungal proteins isolated from a soil sample, and P. chrysogenum HKF2, a strain with carbohydrate-converting activities isolated from a sludge treatment plant, showed strain specific genes. Conclusions: The overall comparison of all available P. chrysogenum genomes indicates that there are a significant number of strain-specific genes, mutations of structural and regulatory genes, gene cluster duplications and DNA fragment translocations. This information provides important leads to improve the biosynthesis of enzymes, antifungal agents, prebiotics or different types of secondary metabolites.
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Affiliation(s)
- Juan F Martín
- Área de Microbiología, Departamento de Biología Molecular, Universidad de León, 24071 León, Spain
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8
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Barreiro C, García-Estrada C. Proteomics and Penicillium chrysogenum: Unveiling the secrets behind penicillin production. J Proteomics 2018; 198:119-131. [PMID: 30414515 DOI: 10.1016/j.jprot.2018.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 10/27/2018] [Accepted: 11/05/2018] [Indexed: 01/29/2023]
Abstract
Discovery, industrial production and clinical applications of penicillin, together with scientific findings on penicillin biosynthesis and its complex regulation, are model milestones of the historical evolution of the most recognized 'magic bullet' against microbial infections available in the worldwide market. Thousands of tons of penicillin produced nowadays are the result of a huge number of technical, industrial and scientific tackled and solved challenges. This combination of, sometimes unsuspected, findings has given Proteomics the chance to support the understanding of the physiology of the high-producing fungal strains and the development of enhanced mutants by means of inverse engineering. Thus, this review, which is part of the special issue entitled "A Tribute to J. Proteomics on its 10th Anniversary", describes how Proteomics has contributed to characterize different aspects related to penicillin production in Penicillium chrosogenum. It covers from global proteome characterizations (intracellular, extracellular and microbodies) to proteome-wide comparative analyses between different penicillin-producing mutant strains and conditions, paying special attention to the methodologies used, as well as to the most important outcomes. As a result, a guide of Proteomics approaches applied to the characterization of penicillin production by P. chrysogenum is detailed in the birthday of the Fleming's most relevant finding. SIGNIFICANCE: Although the discovery of penicillin is celebrating the 90th birthday and its clinical application is worldwide recognized, in fact, semisynthetic penicillins are still one of the most prescribed antibiotics, only the arrival of the post-genomic era during the first decade of the 21st century, and more precisely the Proteomics approaches, have contributed to unveil the industrial secrets behind penicillin production. This review provides relevant information, based on proteomics studies, about the molecular mechanisms responsible for increased penicillin titres, and therefore, may represent a clear model of inverse engineering in microorganisms.
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Affiliation(s)
- Carlos Barreiro
- INBIOTEC (Instituto de Biotecnología de León), Avda. Real 1 - Parque Científico de León, 24006 León, Spain; Departamento de Biología Molecular, Universidad de León, Campus de Ponferrada, Avda. Astorga s/n, 24401 Ponferrada, Spain.
| | - Carlos García-Estrada
- INBIOTEC (Instituto de Biotecnología de León), Avda. Real 1 - Parque Científico de León, 24006 León, Spain; Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
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9
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Guzman‐Chavez F, Salo O, Samol M, Ries M, Kuipers J, Bovenberg RAL, Vreeken RJ, Driessen AJM. Deregulation of secondary metabolism in a histone deacetylase mutant of Penicillium chrysogenum. Microbiologyopen 2018; 7:e00598. [PMID: 29575742 PMCID: PMC6182556 DOI: 10.1002/mbo3.598] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 01/08/2018] [Accepted: 01/12/2018] [Indexed: 11/08/2022] Open
Abstract
The Pc21 g14570 gene of Penicillium chrysogenum encodes an ortholog of a class 2 histone deacetylase termed HdaA which may play a role in epigenetic regulation of secondary metabolism. Deletion of the hdaA gene induces a significant pleiotropic effect on the expression of a set of polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS)-encoding genes. The deletion mutant exhibits a decreased conidial pigmentation that is related to a reduced expression of the PKS gene Pc21 g16000 (pks17) responsible for the production of the pigment precursor naphtha-γ-pyrone. Moreover, the hdaA deletion caused decreased levels of the yellow pigment chrysogine that is associated with the downregulation of the NRPS-encoding gene Pc21 g12630 and associated biosynthetic gene cluster. In contrast, transcriptional activation of the sorbicillinoids biosynthetic gene cluster occurred concomitantly with the overproduction of associated compounds . A new compound was detected in the deletion strain that was observed only under conditions of sorbicillinoids production, suggesting crosstalk between biosynthetic gene clusters. Our present results show that an epigenomic approach can be successfully applied for the activation of secondary metabolism in industrial strains of P. chrysogenum.
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Affiliation(s)
- Fernando Guzman‐Chavez
- Molecular MicrobiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
- Kluyver Centre for Genomics of Industrial FermentationsDelftThe Netherlands
| | - Oleksandr Salo
- Molecular MicrobiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
- Kluyver Centre for Genomics of Industrial FermentationsDelftThe Netherlands
| | - Marta Samol
- Molecular MicrobiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
- Kluyver Centre for Genomics of Industrial FermentationsDelftThe Netherlands
| | - Marco Ries
- Division of Analytical BiosciencesLeiden/Amsterdam Center for Drug ResearchLeidenThe Netherlands
- Netherlands Metabolomics CentreLeiden UniversityLeidenThe Netherlands
| | - Jeroen Kuipers
- Department of Cell biologyUniversity Medical Center GroningenGroningenThe Netherlands
| | - Roel A. L. Bovenberg
- Synthetic Biology and Cell EngineeringGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
- DSM Biotechnology CenterDelftThe Netherlands
| | - Rob J. Vreeken
- Division of Analytical BiosciencesLeiden/Amsterdam Center for Drug ResearchLeidenThe Netherlands
- Netherlands Metabolomics CentreLeiden UniversityLeidenThe Netherlands
- Present address:
Rob J. Vreeken, Discovery SciencesJanssen R &DBeerseBelgium
| | - Arnold J. M. Driessen
- Molecular MicrobiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
- Kluyver Centre for Genomics of Industrial FermentationsDelftThe Netherlands
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10
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Ferreira-Guedes S, Leitão AL. Simultaneous removal of dihydroxybenzenes and toxicity reduction by Penicillium chrysogenum var. halophenolicum under saline conditions. Ecotoxicol Environ Saf 2018; 150:240-250. [PMID: 29288905 DOI: 10.1016/j.ecoenv.2017.12.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 12/17/2017] [Accepted: 12/20/2017] [Indexed: 06/07/2023]
Abstract
The dihydroxybenzenes are widely found in wastewater and usually more than one of these aromatic compounds co-exist as pollutants of water resources. The current study investigated and compared the removal efficiency of hydroquinone, catechol and resorcinol in binary substrate systems under saline conditions by Penicillium chrysogenum var. halophenolicum, to clarify the potential of this fungal strain to degrade these aromatic compounds. Since P. chrysogenum is a known penicillin producer, biosynthetic penicillin genes were examined and antibiotic was quantified in mono and binary dihydroxybenzene systems to elucidate the carbon flux of dihydroxybenzenes metabolism in the P. chrysogenum var. halophenolicum to the secondary metabolism. In binary substrate systems, the three assayed dihydroxybenzene compounds were found to be co-metabolized by fungal strain. The fungal strain preferentially degraded hydroquinone and catechol. Resorcinol was degraded slower and supports higher antibiotic titers than either catechol or hydroquinone. Dihydroxybenzenes were faster removed in mixtures compared to mono substrate systems, except for the case of hydroquinone. In this context, the expression of penicillin biosynthetic gene cluster was not related to the removal of dihydroxybenzenes. Penicillin production was triggered simultaneously or after dihydroxybenzene degradation, but penicillin yields, under these conditions, did not compromise dihydroxybenzene biological treatment. To investigate the decrease in dihydroxybenzenes toxicity due to the fungal activity, viability tests with human colon cancer cells (HCT116) and DNA damage by alkaline comet assays were performed. For all the conditions assays, a decrease in saline medium toxicity was observed, indicating its potential as detoxification agent.
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Affiliation(s)
- Sumaya Ferreira-Guedes
- MEtRICs, Departamento de Ciências e Tecnologia da Biomassa, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Ana Lúcia Leitão
- MEtRICs, Departamento de Ciências e Tecnologia da Biomassa, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal.
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Abstract
Several CRISPR/Cas9 tools have been recently established for precise genome editing in a wide range of filamentous fungi. This genome editing platform offers high flexibility in target selection and the possibility of introducing genetic deletions without the introduction of transgenic sequences . This chapter describes an approach for the transformation of Penicillium chrysogenum protoplasts with preassembled ribonucleoprotein particles (RNPs) consisting of purified Cas9 protein and in vitro transcribed single guide RNA (sgRNA) for the deletion of genome sequences or their replacement with alternative sequences. This method is potentially transferable to all fungal strains where protoplasts can be obtained from.
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Affiliation(s)
- Carsten Pohl
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - László Mózsik
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
| | - Roel A L Bovenberg
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- DSM Biotechnology Center, DSM Food Specialties B.V., Delft, The Netherlands
| | - Yvonne I Nygård
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Chalmers University of Technology, Gothenburg, Sweden
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12
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Yang Y, Zhu N, Yang J, Lin Y, Liu J, Wang R, Wang F, Yuan H. A novel bifunctional acetyl xylan esterase/arabinofuranosidase from Penicillium chrysogenum P33 enhances enzymatic hydrolysis of lignocellulose. Microb Cell Fact 2017; 16:166. [PMID: 28950907 PMCID: PMC5615437 DOI: 10.1186/s12934-017-0777-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/18/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Xylan, the major constituent of hemicellulose, is composed of β-(1,4)-linked xylopyranosyl units that for the backbone, with side chains formed by other chemical moieties such as arabinose, galactose, mannose, ferulic acid and acetyl groups. Acetyl xylan esterases and α-L-arabinofuranosidases are two important accessory enzymes that remove side chain residues from xylan backbones and may act in synergy with other xylanolytic enzymes. Compared with enzymes possessing a single catalytic activity, multifunctional enzymes can achieve lignocellulosic biomass hydrolysis using a less complex mixture of enzymes. RESULTS Here, we cloned an acetyl xylan esterase (PcAxe) from Penicillium chrysogenum P33 and expressed it in Pichia pastoris GS115. The optimal pH and temperature of the recombinant PcAxe (rPcAxe) for 4-nitrophenyl acetate were 7.0 and 40 °C, respectively. rPcAxe is stable across a broad pH range, retaining 100% enzyme activity om pH 6-9 after a 1 h incubation. The enzyme tolerates the presence of a wide range of metal ions. Sequence alignment revealed a GH62 domain exhibiting α-L-arabinofuranosidase activity with pH and temperature optima of pH 7.0 and 50 °C, in addition to the expected esterase domain. rPcAxe displayed significant synergy with a recombinant xylanase, with a degree of synergy of 1.35 for the hydrolysis of delignified corn stover. Release of glucose was increased by 51% from delignified corn stover when 2 mg of a commercial cellulase was replaced by an equivalent amount of rPcAxe, indicating superior hydrolytic efficiency. CONCLUSIONS The novel bifunctional enzyme PcAxe was identified in P. chrysogenum P33. rPcAxe includes a carbohydrate esterase domain and a glycosyl hydrolase family 62 domain. This is the first detailed report on a novel bifunctional enzyme possessing acetyl xylan esterase and α-L-arabinofuranosidase activities. These findings expand our current knowledge of glycoside hydrolases and pave the way for the discovery of similar novel enzymes.
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Affiliation(s)
- Yi Yang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ning Zhu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jinshui Yang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yujian Lin
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jiawen Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ruonan Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Fengqin Wang
- College of Life Science, Henan Agricultural University, Zhengzhou, China
| | - Hongli Yuan
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- National Energy R & D Center for Non-food Biomass, China Agricultural University, Beijing, China
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13
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Guzmán-Chávez F, Salo O, Nygård Y, Lankhorst PP, Bovenberg RAL, Driessen AJM. Mechanism and regulation of sorbicillin biosynthesis by Penicillium chrysogenum. Microb Biotechnol 2017; 10:958-968. [PMID: 28618182 PMCID: PMC5481523 DOI: 10.1111/1751-7915.12736] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 04/25/2017] [Accepted: 04/28/2017] [Indexed: 11/29/2022] Open
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-coloured 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, sorbicillinoid 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 enzymes 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. Deletion of either of the two pks genes not only impacted the overall production 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 sorbicillinoid pathway is regulated through a novel autoinduction mechanism where sorbicillinoids activate transcription.
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Affiliation(s)
- Fernando Guzmán-Chávez
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Oleksandr Salo
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Yvonne Nygård
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Peter P Lankhorst
- Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Roel A L Bovenberg
- Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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14
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Terfehr D, Dahlmann TA, Kück U. Transcriptome analysis of the two unrelated fungal β-lactam producers Acremonium chrysogenum and Penicillium chrysogenum: Velvet-regulated genes are major targets during conventional strain improvement programs. BMC Genomics 2017; 18:272. [PMID: 28359302 PMCID: PMC5374653 DOI: 10.1186/s12864-017-3663-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 03/25/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Cephalosporins and penicillins are the most frequently used β-lactam antibiotics for the treatment of human infections worldwide. The main industrial producers of these antibiotics are Acremonium chrysogenum and Penicillium chrysogenum, two taxonomically unrelated fungi. Both were subjects of long-term strain development programs to reach economically relevant antibiotic titers. It is so far unknown, whether equivalent changes in gene expression lead to elevated antibiotic titers in production strains. RESULTS Using the sequence of PcbC, a key enzyme of β-lactam antibiotic biosynthesis, from eighteen different pro- and eukaryotic microorganisms, we have constructed a phylogenetic tree to demonstrate the distant relationship of both fungal producers. To address the question whether both fungi have undergone similar genetic adaptions, we have performed a comparative gene expression analysis of wild-type and production strains. We found that strain improvement is associated with the remodeling of the transcriptional landscape in both fungi. In P. chrysogenum, 748 genes showed differential expression, while 1572 genes from A. chrysogenum are differentially expressed in the industrial strain. Common in both fungi is the upregulation of genes belonging to primary and secondary metabolism, notably those involved in precursor supply for β-lactam production. Other genes not essential for β-lactam production are downregulated with a preference for those responsible for transport processes or biosynthesis of other secondary metabolites. Transcriptional regulation was shown to be an important parameter during strain improvement in different organisms. We therefore investigated deletion strains of the major transcriptional regulator velvet from both production strains. We identified 567 P. chrysogenum and 412 A. chrysogenum Velvet target genes. In both deletion strains, approximately 50% of all secondary metabolite cluster genes are differentially regulated, including β-lactam biosynthesis genes. Most importantly, 35-57% of Velvet target genes are among those that showed differential expression in both improved industrial strains. CONCLUSIONS The major finding of our comparative transcriptome analysis is that strain improvement programs in two unrelated fungal β-lactam antibiotic producers alter the expression of target genes of Velvet, a global regulator of secondary metabolism. From these results, we conclude that regulatory alterations are crucial contributing factors for improved β-lactam antibiotic titers during strain improvement in both fungi.
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Affiliation(s)
- Dominik Terfehr
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-University Bochum, Universitätsstr. 150, Bochum, 44780, Germany
| | - Tim A Dahlmann
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-University Bochum, Universitätsstr. 150, Bochum, 44780, Germany
| | - Ulrich Kück
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-University Bochum, Universitätsstr. 150, Bochum, 44780, Germany.
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15
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Jónás Á, Fekete E, Németh Z, Flipphi M, Karaffa L. D-galactose catabolism in Penicillium chrysogenum: Expression analysis of the structural genes of the Leloir pathway. Acta Biol Hung 2016; 67:318-32. [PMID: 27630054 DOI: 10.1556/018.67.2016.3.9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In this study, we analyzed the expression of the structural genes encoding the five enzymes comprising the Leloir pathway of D-galactose catabolism in the industrial cell factory Penicillium chrysogenum on various carbon sources. The genome of P. chrysogenum contains a putative galactokinase gene at the annotated locus Pc13g10140, the product of which shows strong structural similarity to yeast galactokinase that was expressed on lactose and D-galactose only. The expression profile of the galactose-1-phosphate uridylyl transferase gene at annotated locus Pc15g00140 was essentially similar to that of galactokinase. This is in contrast to the results from other fungi such as Aspergillus nidulans, Trichoderma reesei and A. niger, where the ortholog galactokinase and galactose-1-phosphate uridylyl transferase genes were constitutively expressed. As for the UDP-galactose-4-epimerase encoding gene, five candidates were identified. We could not detect Pc16g12790, Pc21g12170 and Pc20g06140 expression on any of the carbon sources tested, while for the other two loci (Pc21g10370 and Pc18g01080) transcripts were clearly observed under all tested conditions. Like the 4-epimerase specified at locus Pc21g10370, the other two structural Leloir pathway genes - UDP-glucose pyrophosphorylase (Pc21g12790) and phosphoglucomutase (Pc18g01390) - were expressed constitutively at high levels as can be expected from their indispensable function in fungal cell wall formation.
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Affiliation(s)
- Ágota Jónás
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen , H-4032, P.O. Box 64, Debrecen , Hungary
| | - Erzsébet Fekete
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen , H-4032, P.O. Box 64, Debrecen , Hungary
| | - Zoltán Németh
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen , H-4032, P.O. Box 64, Debrecen , Hungary
| | - Michel Flipphi
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen , H-4032, P.O. Box 64, Debrecen , Hungary
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen , H-4032, P.O. Box 64, Debrecen , Hungary
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16
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Abstract
CRISPR/Cas9 based systems have emerged as versatile platforms for precision genome editing in a wide range of organisms. Here we have developed powerful CRISPR/Cas9 tools for marker-based and marker-free genome modifications in Penicillium chrysogenum, a model filamentous fungus and industrially relevant cell factory. The developed CRISPR/Cas9 toolbox is highly flexible and allows editing of new targets with minimal cloning efforts. The Cas9 protein and the sgRNA can be either delivered during transformation, as preassembled CRISPR-Cas9 ribonucleoproteins (RNPs) or expressed from an AMA1 based plasmid within the cell. The direct delivery of the Cas9 protein with in vitro synthesized sgRNA to the cells allows for a transient method for genome engineering that may rapidly be applicable for other filamentous fungi. The expression of Cas9 from an AMA1 based vector was shown to be highly efficient for marker-free gene deletions.
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Affiliation(s)
- C Pohl
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - J A K W Kiel
- Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - A J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - R A L Bovenberg
- Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- DSM Biotechnology Centre , Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands
| | - Y Nygård
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- DSM Biotechnology Centre , Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands
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17
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Sathishkumar Y, Krishnaraj C, Rajagopal K, Sen D, Lee YS. High throughput de novo RNA sequencing elucidates novel responses in Penicillium chrysogenum under microgravity. Bioprocess Biosyst Eng 2015; 39:223-31. [PMID: 26603994 DOI: 10.1007/s00449-015-1506-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/10/2015] [Indexed: 12/24/2022]
Abstract
In this study, the transcriptional alterations in Penicillium chrysogenum under simulated microgravity conditions were analyzed for the first time using an RNA-Seq method. The increasing plethora of eukaryotic microbial flora inside the spaceship demands the basic understanding of fungal biology in the absence of gravity vector. Penicillium species are second most dominant fungal contaminant in International Space Station. Penicillium chrysogenum an industrially important organism also has the potential to emerge as an opportunistic pathogen for the astronauts during the long-term space missions. But till date, the cellular mechanisms underlying the survival and adaptation of Penicillium chrysogenum to microgravity conditions are not clearly elucidated. A reference genome for Penicillium chrysogenum is not yet available in the NCBI database. Hence, we performed comparative de novo transcriptome analysis of Penicillium chrysogenum grown under microgravity versus normal gravity. In addition, the changes due to microgravity are documented at the molecular level. Increased response to the environmental stimulus, changes in the cell wall component ABC transporter/MFS transporters are noteworthy. Interestingly, sustained increase in the expression of Acyl-coenzyme A: isopenicillin N acyltransferase (Acyltransferase) under microgravity revealed the significance of gravity in the penicillin production which could be exploited industrially.
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Affiliation(s)
- Yesupatham Sathishkumar
- Department of Forest Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, 561-756, Republic of Korea.
| | - Chandran Krishnaraj
- Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, 561-756, Republic of Korea
| | | | - Dwaipayan Sen
- School of Biosciences and Technology, VIT University, Vellore, 632014, India
- Cellular and Molecular Therapeutics Laboratory, Centre for Biomaterials, Cellular and Molecular Theranostics, School of Biosciences and Technology, VIT University, Vellore, 632014, India
| | - Yang Soo Lee
- Department of Forest Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, 561-756, Republic of Korea.
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18
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Böhm J, Dahlmann TA, Gümüşer H, Kück U. A MAT1-2 wild-type strain from Penicillium chrysogenum: functional mating-type locus characterization, genome sequencing and mating with an industrial penicillin-producing strain. Mol Microbiol 2015; 95:859-74. [PMID: 25521009 PMCID: PMC4357460 DOI: 10.1111/mmi.12909] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2014] [Indexed: 01/07/2023]
Abstract
In heterothallic ascomycetes, mating is controlled by two nonallelic idiomorphs that determine the 'sex' of the corresponding strains. We recently discovered mating-type loci and a sexual life cycle in the penicillin-producing fungus, Penicillium chrysogenum. All industrial penicillin production strains worldwide are derived from a MAT1-1 isolate. No MAT1-2 strain has been investigated in detail until now. Here, we provide the first functional analysis of a MAT1-2 locus from a wild-type strain. Similar to MAT1-1, the MAT1-2 locus has functions beyond sexual development. Unlike MAT1-1, the MAT1-2 locus affects germination and surface properties of conidiospores and controls light-dependent asexual sporulation. Mating of the MAT1-2 wild type with a MAT1-1 high penicillin producer generated sexual spores. We determined the genomic sequences of parental and progeny strains using next-generation sequencing and found evidence for genome-wide recombination. SNP calling showed that derived industrial strains had an uneven distribution of point mutations compared with the wild type. We found evidence for meiotic recombination in all chromosomes. Our results point to a strategy combining the use of mating-type genes, genetics, and next-generation sequencing to optimize conventional strain improvement methods.
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Affiliation(s)
- Julia Böhm
- Christian Doppler Laboratory for Fungal Biotechnology, Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität BochumUniversitätsstr. 150, D-44780, Bochum, Germany
| | - Tim A Dahlmann
- Christian Doppler Laboratory for Fungal Biotechnology, Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität BochumUniversitätsstr. 150, D-44780, Bochum, Germany
| | - Hendrik Gümüşer
- Christian Doppler Laboratory for Fungal Biotechnology, Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität BochumUniversitätsstr. 150, D-44780, Bochum, Germany
| | - Ulrich Kück
- Christian Doppler Laboratory for Fungal Biotechnology, Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität BochumUniversitätsstr. 150, D-44780, Bochum, Germany
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19
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Pérez EA, Fernández FJ, Fierro F, Mejía A, Marcos AT, Martín JF, Barrios-González J. Yeast HXK2 gene reverts glucose regulation mutation of penicillin biosynthesis in P. chrysogenum. Braz J Microbiol 2014; 45:873-83. [PMID: 25477921 PMCID: PMC4204972 DOI: 10.1590/s1517-83822014000300017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 03/14/2014] [Indexed: 11/25/2022] Open
Abstract
The mutant Penicillium chrysogenum strain dogR5, derived from strain AS-P-78, does not respond to glucose regulation of penicillin biosynthesis and β-galactosidase, and is partially deficient in D-glucose phosphorilating activity. We have transformed strain dogR5 with the (hexokinase) hxk2 gene from Saccharomyces cerevisiae. Transformants recovered glucose control of penicillin biosynthesis in different degrees, and acquired a hexokinase (fructose phosphorylating) activity absent in strains AS- P-78 and dogR5. Interestingly, they also recovered glucose regulation of β-galactosidase. On the other hand, glucokinase activity was affected in different ways in the transformants; one of which showed a lower activity than the parental dogR5, but normal glucose regulation of penicillin biosynthesis. Our results show that Penicillium chrysogenum AS-P-78 and dogR5 strains lack hexokinase, and suggest that an enzyme with glucokinase activity is involved in glucose regulation of penicillin biosynthesis and β-galactosidase, thus signaling glucose in both primary and secondary metabolism; however, catalytic and signaling activities seem to be independent.
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Affiliation(s)
- Edmundo A. Pérez
- Laboratorio de Ingeniería Genética y Metabolitos SecundariosDepartamento de BiotecnologíaUniversidad Autónoma MetropolitanaMexico D.F.MexicoLaboratorio de Ingeniería Genética y Metabolitos Secundarios, Departamento de Biotecnología, Universidad Autónoma Metropolitana, Mexico D.F., Mexico.
| | - Francisco J. Fernández
- Laboratorio de Ingeniería Genética y Metabolitos SecundariosDepartamento de BiotecnologíaUniversidad Autónoma MetropolitanaMexico D.F.MexicoLaboratorio de Ingeniería Genética y Metabolitos Secundarios, Departamento de Biotecnología, Universidad Autónoma Metropolitana, Mexico D.F., Mexico.
| | - Francisco Fierro
- Laboratorio de Ingeniería Genética y Metabolitos SecundariosDepartamento de BiotecnologíaUniversidad Autónoma MetropolitanaMexico D.F.MexicoLaboratorio de Ingeniería Genética y Metabolitos Secundarios, Departamento de Biotecnología, Universidad Autónoma Metropolitana, Mexico D.F., Mexico.
| | - Armando Mejía
- Laboratorio de Ingeniería Genética y Metabolitos SecundariosDepartamento de BiotecnologíaUniversidad Autónoma MetropolitanaMexico D.F.MexicoLaboratorio de Ingeniería Genética y Metabolitos Secundarios, Departamento de Biotecnología, Universidad Autónoma Metropolitana, Mexico D.F., Mexico.
| | - Ana T. Marcos
- Instituto de Biotecnología de LeónLeónSpainInstituto de Biotecnología de León, León, Spain.
| | - Juan F. Martín
- Instituto de Biotecnología de LeónLeónSpainInstituto de Biotecnología de León, León, Spain.
- Área de MicrobiologíaFacultad de Ciencias Biológicas y AmbientalesUniversidad de LeónLeónSpainÁrea de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, León, Spain.
| | - Javier Barrios-González
- Laboratorio de Ingeniería Genética y Metabolitos SecundariosDepartamento de BiotecnologíaUniversidad Autónoma MetropolitanaMexico D.F.MexicoLaboratorio de Ingeniería Genética y Metabolitos Secundarios, Departamento de Biotecnología, Universidad Autónoma Metropolitana, Mexico D.F., Mexico.
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20
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Wong VL, Ellison CE, Eisen MB, Pachter L, Brem RB. Structural variation among wild and industrial strains of Penicillium chrysogenum. PLoS One 2014; 9:e96784. [PMID: 24824901 PMCID: PMC4019546 DOI: 10.1371/journal.pone.0096784] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 04/11/2014] [Indexed: 11/24/2022] Open
Abstract
Strain selection and strain improvement are the first, and arguably most important, steps in the industrial production of biological compounds by microorganisms. While traditional methods of mutagenesis and selection have been effective in improving production of compounds at a commercial scale, the genetic changes underpinning the altered phenotypes have remained largely unclear. We utilized high-throughput Illumina short read sequencing of a wild Penicillium chrysogenum strain in order to make whole genome comparisons to a sequenced improved strain (WIS 54–1255). We developed an assembly-free method of identifying chromosomal rearrangements and validated the in silico predictions with a PCR-based assay and Sanger sequencing. Despite many rounds of mutagen treatment and artificial selection, WIS 54–1255 differs from its wild progenitor at only one of the identified rearrangements. We suggest that natural variants predisposed for high penicillin production were instrumental in the success of WIS 54–1255 as an industrial strain. In addition to finding a previously published inversion in the penicillin biosynthesis cluster, we located several genes related to penicillin production associated with these rearrangements. By comparing the configuration of rearrangement events among several historically important strains known to be high penicillin producers to a collection of recently isolated wild strains, we suggest that wild strains with rearrangements similar to those in known high penicillin producers may be viable candidates for further improvement efforts.
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Affiliation(s)
- Valerie L. Wong
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
- * E-mail:
| | - Christopher E. Ellison
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Michael B. Eisen
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Lior Pachter
- Departments of Mathematics, Molecular and Cell Biology, and Electrical Engineering and Computer Science, University of California Berkeley, Berkeley, California, United States of America
| | - Rachel B. Brem
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
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21
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Cepeda-García C, Domínguez-Santos R, García-Rico RO, García-Estrada C, Cajiao A, Fierro F, Martín JF. Direct involvement of the CreA transcription factor in penicillin biosynthesis and expression of the pcbAB gene in Penicillium chrysogenum. Appl Microbiol Biotechnol 2014; 98:7113-24. [PMID: 24818689 DOI: 10.1007/s00253-014-5760-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 04/03/2014] [Accepted: 04/05/2014] [Indexed: 01/29/2023]
Abstract
The transcription factor CreA is the main regulator responsible for carbon repression in filamentous fungi. CreA is a wide domain regulator that binds to regulatory elements in the promoters of target genes to repress their transcription. Penicillin biosynthesis and the expression of penicillin biosynthetic genes are subject to carbon repression. However, evidence of the participation of CreA in this regulation is still lacking, and previous studies on the promoter of the pcbC gene of Aspergillus nidulans indicated the lack of involvement of CreA in its regulation. Here we present clear evidence of the participation of CreA in carbon repression of penicillin biosynthesis and expression of the pcbAB gene, encoding the first enzyme of the pathway, in Penicillium chrysogenum. Mutations in cis of some of the putative CreA binding sites present in the pcbAB gene promoter fused to a reporter gene caused an important increase in the measured enzyme activity in glucose-containing medium, whereas activity in the medium with lactose was not affected. An RNAi strategy was used to attenuate the expression of the creA gene. Transformants expressing a small interfering RNA for creA showed higher penicillin production, and this increase was more evident when glucose was used as carbon source. These results confirm that CreA plays an important role in the regulation of penicillin biosynthesis in P. chrysogenum and opens the possibility of its utilization to improve the industrial production of this antibiotic.
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Affiliation(s)
- Cristina Cepeda-García
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, León, Spain
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Wang FQ, Zhong J, Zhao Y, Xiao J, Liu J, Dai M, Zheng G, Zhang L, Yu J, Wu J, Duan B. Genome sequencing of high-penicillin producing industrial strain of Penicillium chrysogenum. BMC Genomics 2014; 15 Suppl 1:S11. [PMID: 24564352 PMCID: PMC4046689 DOI: 10.1186/1471-2164-15-s1-s11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Due to the importance of Penicillium chrysogenum holding in medicine, the genome of low-penicillin producing laboratorial strain Wisconsin54-1255 had been sequenced and fully annotated. Through classical mutagenesis of Wisconsin54-1255, product titers and productivities of penicillin have dramatically increased, but what underlying genome structural variations is still little known. Therefore, genome sequencing of a high-penicillin producing industrial strain is very meaningful. RESULTS To reveal more insights into the genome structural variations of high-penicillin producing strain, we sequenced an industrial strain P. chrysogenum NCPC10086. By whole genome comparative analysis, we observed a large number of mutations, insertions and deletions, and structural variations. There are 69 new genes that not exist in the genome sequence of Wisconsin54-1255 and some of them are involved in energy metabolism, nitrogen metabolism and glutathione metabolism. Most importantly, we discovered a 53.7 Kb "new shift fragment" in a seven copies of determinative penicillin biosynthesis cluster in NCPC10086 and the arrangement type of amplified region is unique. Moreover, we presented two large-scale translocations in NCPC10086, containing genes involved energy, nitrogen metabolism and peroxysome pathway. At last, we found some non-synonymous mutations in the genes participating in homogentisate pathway or working as regulators of penicillin biosynthesis. CONCLUSIONS We provided the first high-quality genome sequence of industrial high-penicillin strain of P. chrysogenum and carried out a comparative genome analysis with a low-producing experimental strain. The genomic variations we discovered are related with energy metabolism, nitrogen metabolism and so on. These findings demonstrate the potential information for insights into the high-penicillin yielding mechanism and metabolic engineering in the future.
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Affiliation(s)
- Fu-Qiang Wang
- />New Drug Research and Development Center of North China Pharmaceutical Group Corporation, National Engineering Research Center of Microbial Medicine, Hebei Industry Microbial Metabolic Engineering & Technology Research Center, Shijiazhuang, Hebei 050015 China
| | - Jun Zhong
- />CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
- />University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Ying Zhao
- />New Drug Research and Development Center of North China Pharmaceutical Group Corporation, National Engineering Research Center of Microbial Medicine, Hebei Industry Microbial Metabolic Engineering & Technology Research Center, Shijiazhuang, Hebei 050015 China
| | - Jingfa Xiao
- />CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Jing Liu
- />New Drug Research and Development Center of North China Pharmaceutical Group Corporation, National Engineering Research Center of Microbial Medicine, Hebei Industry Microbial Metabolic Engineering & Technology Research Center, Shijiazhuang, Hebei 050015 China
| | - Meng Dai
- />New Drug Research and Development Center of North China Pharmaceutical Group Corporation, National Engineering Research Center of Microbial Medicine, Hebei Industry Microbial Metabolic Engineering & Technology Research Center, Shijiazhuang, Hebei 050015 China
| | - Guizhen Zheng
- />New Drug Research and Development Center of North China Pharmaceutical Group Corporation, National Engineering Research Center of Microbial Medicine, Hebei Industry Microbial Metabolic Engineering & Technology Research Center, Shijiazhuang, Hebei 050015 China
| | - Li Zhang
- />New Drug Research and Development Center of North China Pharmaceutical Group Corporation, National Engineering Research Center of Microbial Medicine, Hebei Industry Microbial Metabolic Engineering & Technology Research Center, Shijiazhuang, Hebei 050015 China
| | - Jun Yu
- />CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Jiayan Wu
- />CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Baoling Duan
- />New Drug Research and Development Center of North China Pharmaceutical Group Corporation, National Engineering Research Center of Microbial Medicine, Hebei Industry Microbial Metabolic Engineering & Technology Research Center, Shijiazhuang, Hebei 050015 China
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Kurzątkowski W, Staniszewska M, Bondaryk M, Gębska-Kuczerowska A. Compartmentalization in penicillin G biosynthesis by Penicillium chrysogenum PQ-96. Pol J Microbiol 2014; 63:399-408. [PMID: 25804059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023] Open
Abstract
The arrangement of organelles in the sub-apical productive non-growing vacuolated hyphal cells of the high- and the low-penicillin-pro- ducing strains Penicillium chrysogenum was compared using transmission electron microscopy. In the productive cells of the high-yielding strain the endoplasmic reticulum and the polyribosomes with associated peroxisomes are frequently arranged at the periphery of the cytoplasm and around the vacuoles. At the high activity of penicillin G biosynthesis the immuno-label of the cytosolic isopenicillin N synthase is concentrated at the polyribosomes arranged in the peripheral cytoplasm and along the tonoplast as well as around the peroxisomes. On the basis of the obtained results the compartmentalization of the pathway of penicillin G biosymthesis is discussed. The obtained results support the phenylacetic acid detoxification hypothesis of penicillin G biosynthesis.
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Ries MI, Ali H, Lankhorst PP, Hankemeier T, Bovenberg RAL, Driessen AJM, Vreeken RJ. Novel key metabolites reveal further branching of the roquefortine/meleagrin biosynthetic pathway. J Biol Chem 2013; 288:37289-95. [PMID: 24225953 PMCID: PMC3873581 DOI: 10.1074/jbc.m113.512665] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 11/11/2013] [Indexed: 11/06/2022] Open
Abstract
Metabolic profiling and structural elucidation of novel secondary metabolites obtained from derived deletion strains of the filamentous fungus Penicillium chrysogenum were used to reassign various previously ascribed synthetase genes of the roquefortine/meleagrin pathway to their corresponding products. Next to the structural characterization of roquefortine F and neoxaline, which are for the first time reported for P. chrysogenum, we identified the novel metabolite roquefortine L, including its degradation products, harboring remarkable chemical structures. Their biosynthesis is discussed, questioning the exclusive role of glandicoline A as key intermediate in the pathway. The results reveal that further enzymes of this pathway are rather unspecific and catalyze more than one reaction, leading to excessive branching in the pathway with meleagrin and neoxaline as end products of two branches.
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Affiliation(s)
- Marco I. Ries
- From the Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Einsteinweg 55, 2333CC Leiden
| | - Hazrat Ali
- the Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747AG Groningen
- the Kluyver Centre for Genomics of Industrial Fermentations, Julianalaan 67, 2628BC Delft
| | | | - Thomas Hankemeier
- From the Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Einsteinweg 55, 2333CC Leiden
- the Netherlands Metabolomics Centre, Leiden University, Einsteinweg 55, 2333CC Leiden, and
| | - Roel A. L. Bovenberg
- the DSM Biotechnology Center, Alexander Fleminglaan 1, 2613AX Delft
- the Department of Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Arnold J. M. Driessen
- the Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747AG Groningen
- the Kluyver Centre for Genomics of Industrial Fermentations, Julianalaan 67, 2628BC Delft
| | - Rob J. Vreeken
- From the Division of Analytical Biosciences, Leiden Academic Centre for Drug Research, Einsteinweg 55, 2333CC Leiden
- the Netherlands Metabolomics Centre, Leiden University, Einsteinweg 55, 2333CC Leiden, and
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25
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de Boer P, Bronkhof J, Dukiќ K, Kerkman R, Touw H, van den Berg M, Offringa R. Efficient gene targeting in Penicillium chrysogenum using novel Agrobacterium-mediated transformation approaches. Fungal Genet Biol 2013; 61:9-14. [PMID: 23994321 DOI: 10.1016/j.fgb.2013.08.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 07/28/2013] [Accepted: 08/19/2013] [Indexed: 11/19/2022]
Abstract
The industrial production of β-lactam antibiotics by Penicillium chrysogenum has increased tremendously over the last decades, however, further optimization via classical strain and process improvement has reached its limits. The availability of the genome sequence provides new opportunities for directed strain improvement, but this requires the establishment of an efficient gene targeting (GT) system. Recently, mutations affecting the non-homologous end joining (NHEJ) pathway were shown to increase GT efficiencies following PEG-mediated DNA transfer in P. chrysogenum from 1% to 50%. Apart from direct DNA transfer many fungi can efficiently be transformed using the T-DNA transfer system of the soil bacterium Agrobacterium tumefaciens, however, for P. chrysogenum no robust system for Agrobacterium-mediated transformation was available. We obtained efficient AMT of P. chrysogenum spores with the nourseothricin acetyltransferase gene as selection marker, and using this system we investigated if AMT in a NHEJ mutant background could further enhance GT efficiencies. In general, AMT resulted in higher GT efficiencies than direct DNA transfer, although the final frequencies depended on the Agrobacterium strain and plasmid backbone used. Providing overlapping and complementing fragments on two different plasmid backbones via the same Agrobacterium host was shown to be most effective. This so-called split-marker or bi-partite method resulted in highly efficient GT (>97%) almost exclusively without additional ectopic T-DNA insertions. As this method provides for an efficient GT method independent of protoplasts, it can be applied to other fungi for which no protoplasts can be generated or for which protoplast transformation leads to varying results.
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Affiliation(s)
- Paulo de Boer
- Add2X Biosciences B.V., Sylviusweg 72, 2333 BE Leiden, The Netherlands.
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26
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Ali H, Ries MI, Nijland JG, Lankhorst PP, Hankemeier T, Bovenberg RAL, Vreeken RJ, Driessen AJM. A branched biosynthetic pathway is involved in production of roquefortine and related compounds in Penicillium chrysogenum. PLoS One 2013; 8:e65328. [PMID: 23776469 PMCID: PMC3680398 DOI: 10.1371/journal.pone.0065328] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 04/24/2013] [Indexed: 11/19/2022] Open
Abstract
Profiling and structural elucidation of secondary metabolites produced by the filamentous fungus Penicillium chrysogenum and derived deletion strains were used to identify the various metabolites and enzymatic steps belonging to the roquefortine/meleagrin pathway. Major abundant metabolites of this pathway were identified as histidyltryptophanyldiketopiperazine (HTD), dehydrohistidyltryptophanyldi-ketopiperazine (DHTD), roquefortine D, roquefortine C, glandicoline A, glandicoline B and meleagrin. Specific genes could be assigned to each enzymatic reaction step. The nonribosomal peptide synthetase RoqA accepts L-histidine and L-tryptophan as substrates leading to the production of the diketopiperazine HTD. DHTD, previously suggested to be a degradation product of roquefortine C, was found to be derived from HTD involving the cytochrome P450 oxidoreductase RoqR. The dimethylallyltryptophan synthetase RoqD prenylates both HTD and DHTD yielding directly the products roquefortine D and roquefortine C without the synthesis of a previously suggested intermediate and the involvement of RoqM. This leads to a branch in the otherwise linear pathway. Roquefortine C is subsequently converted into glandicoline B with glandicoline A as intermediates, involving two monooxygenases (RoqM and RoqO) which were mixed up in an earlier attempt to elucidate the biosynthetic pathway. Eventually, meleagrin is produced from glandicoline B involving a methyltransferase (RoqN). It is concluded that roquefortine C and meleagrin are derived from a branched biosynthetic pathway.
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Affiliation(s)
- Hazrat Ali
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentations, Delft, The Netherlands
| | - Marco I. Ries
- Division of Analytical Biosciences, Leiden/Amsterdam Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Jeroen G. Nijland
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentations, Delft, The Netherlands
| | | | - Thomas Hankemeier
- Division of Analytical Biosciences, Leiden/Amsterdam Center for Drug Research, Leiden University, Leiden, The Netherlands
- Netherlands Metabolomics Centre, Leiden University, Leiden, The Netherlands
| | - Roel A. L. Bovenberg
- DSM Biotechnology Center, Delft, The Netherlands
- Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Rob J. Vreeken
- Division of Analytical Biosciences, Leiden/Amsterdam Center for Drug Research, Leiden University, Leiden, The Netherlands
- Netherlands Metabolomics Centre, Leiden University, Leiden, The Netherlands
| | - Arnold J. M. Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentations, Delft, The Netherlands
- * E-mail:
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Chen M, Qin Y, Cao Q, Liu G, Li J, Li Z, Zhao J, Qu Y. Promotion of extracellular lignocellulolytic enzymes production by restraining the intracellular β-glucosidase in Penicillium decumbens. Bioresour Technol 2013; 137:33-40. [PMID: 23584406 DOI: 10.1016/j.biortech.2013.03.099] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 03/10/2013] [Accepted: 03/12/2013] [Indexed: 05/05/2023]
Abstract
In this study, the functions of β-glucosidases in regulation of the lignocellulolytic enzymes production in Penicillium decumbens 114-2 were investigated. The major extracellular β-glucosidase gene bgl1 and the major intracellular β-glucosidase gene bgl2 were deleted in P. decumbens 114-2 respectively. In Δbgl2, the production of extracellular lignocellulolytic enzymes (including endoglucanases, cellobiohydrolases and xylanases) on insoluble cellulose was significantly promoted, while in Δbgl1 there was no any difference compared with that of 114-2. The enhancement of the production of lignocellulolytic enzymes in Δbgl2 was likely attributed to the accumulation of intracellular cellobiose. Induction experiment in Δbgl1Δbgl2 showed that cellobiose was an inducer of lignocellulolytic enzymes expression in P. decumbens 114-2, and the induction was unrelated to the formation, if any, of gentiobiose or sophorose from cellobiose.
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Affiliation(s)
- Mei Chen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, PR China
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28
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Kopke K, Hoff B, Bloemendal S, Katschorowski A, Kamerewerd J, Kück U. Members of the Penicillium chrysogenum velvet complex play functionally opposing roles in the regulation of penicillin biosynthesis and conidiation. Eukaryot Cell 2013; 12:299-310. [PMID: 23264641 PMCID: PMC3571298 DOI: 10.1128/ec.00272-12] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 12/12/2012] [Indexed: 02/08/2023]
Abstract
A velvet multisubunit complex was recently detected in the filamentous fungus Penicillium chrysogenum, the major industrial producer of the β-lactam antibiotic penicillin. Core components of this complex are P. chrysogenum VelA (PcVelA) and PcLaeA, which regulate secondary metabolite production, hyphal morphology, conidiation, and pellet formation. Here we describe the characterization of PcVelB, PcVelC, and PcVosA as novel subunits of this velvet complex. Using yeast two-hybrid analysis and bimolecular fluorescence complementation (BiFC), we demonstrate that all velvet proteins are part of an interaction network. Functional analyses using single- and double-knockout strains clearly indicate that velvet subunits have opposing roles in the regulation of penicillin biosynthesis and light-dependent conidiation. PcVelC, together with PcVelA and PcLaeA, activates penicillin biosynthesis, while PcVelB represses this process. In contrast, PcVelB and PcVosA promote conidiation, while PcVelC has an inhibitory effect. Our genetic analyses further show that light-dependent spore formation depends not only on PcVelA but also on PcVelB and PcVosA. The results provided here contribute to our fundamental understanding of the function of velvet subunits as part of a regulatory network mediating signals responsible for morphology and secondary metabolism and will be instrumental in generating mutants with newly derived properties that are relevant to strain improvement programs.
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Affiliation(s)
- Katarina Kopke
- Christian Doppler Laboratory for Fungal Biotechnology, Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Bochum, Germany
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Song N, Wang F, Zhang C, Tang S, Guo J, Ju X, Smith DL. Fungal inoculation and elevated CO2 mediate growth of Lolium mutiforum and Phytolacca americana, metal uptake, and metal bioavailability in metal-contaminated soil: evidence from DGT measurement. Int J Phytoremediation 2013; 15:268-82. [PMID: 23488012 DOI: 10.1080/15226514.2012.694500] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Fungal inoculation and elevated CO2 may mediate plant growth and uptake of heavy metals, but little evidence from Diffusive Gradients in Thin-films (DGT) measurement has been obtained to characterize the process. Lolium mutiforum and Phytolacca americana were grown at ambient and elevated CO2 on naturally Cd and Pb contaminated soils inoculated with and without Trichoderma asperellum strain C3 or Penicillium chrysogenum strain D4, to investigate plant growth, metal uptake, and metal bioavailability responses. Fungal inoculation increased plant biomass and shoot/root Cd and Pb concentrations. Elevated CO2 significantly increased plants biomass, but decreased Cd and Pb concentrations in shoot/root to various extents, leading to a metal dilution phenomenon. Total Cd and Pb uptake by plants, and DGT-measured Cd and Pb concentrations in rhizosphere soils, were higher in all fungal inoculation and elevated CO2 treatments than control treatments, with the combined treatments having more influence than either treatment alone. Metal dilution phenomenon occurred because the increase in DGT-measured bioavailable metal pools in plant rhizosphere due to elevated CO2 was unable to match the increase in requirement for plant uptake of metals due to plant biomass increase.
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Affiliation(s)
- Ningning Song
- Centre for Research in Ecotoxicology and Environmental Remediation, Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin 300191, P. R. China
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Galgóczy L, Virágh M, Kovács L, Tóth B, Papp T, Vágvölgyi C. Antifungal peptides homologous to the Penicillium chrysogenum antifungal protein (PAF) are widespread among Fusaria. Peptides 2013; 39:131-7. [PMID: 23174348 DOI: 10.1016/j.peptides.2012.10.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 10/09/2012] [Accepted: 10/10/2012] [Indexed: 02/07/2023]
Abstract
Putative antifungal peptide encoding genes containing Penicillium chrysogenum antifungal protein (PAF) characteristic amino acid motifs were identified in 15 Fusarium isolates, representing 10 species. Based on the predicted sequences of mature peptides, discrepancy in one, two or three amino acids was observed between them. Phylogenetic investigations revealed that they show high amino acid sequence similarity to PAF and they belong to the group of fungal derived antifungal peptides with PAF-cluster. Ten from the 15 partially purified <10 kDa peptide fraction of Fusarium ferment broths showed antifungal activity. The presence of approximately 6.3 kDa molecular weight peptides was detected in all of the antifungally active ferment broths, and this peptide was isolated and purified from Fusarium polyphilaidicum. The minimal inhibitiory concentrations of F. polyphilaidicum antifungal protein (FPAP) were determined against different filamentous fungi, yeasts and bacteria. Filamentous fungal species were the most susceptible to FPAF, but some yeasts were also slightly sensitive.
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Affiliation(s)
- László Galgóczy
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary.
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Fernández-Aguado M, Ullán RV, Teijeira F, Rodríguez-Castro R, Martín JF. The transport of phenylacetic acid across the peroxisomal membrane is mediated by the PaaT protein in Penicillium chrysogenum. Appl Microbiol Biotechnol 2012; 97:3073-84. [PMID: 23053082 DOI: 10.1007/s00253-012-4425-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 09/05/2012] [Accepted: 09/06/2012] [Indexed: 11/26/2022]
Abstract
Penicillium chrysogenum, an industrial microorganism used worldwide for penicillin production, is an excellent model to study the biochemistry and the cell biology of enzymes involved in the synthesis of secondary metabolites. The well-known peroxisomal location of the last two steps of penicillin biosynthesis (phenylacetyl-CoA ligase and isopenicillin N acyltransferase) requires the import into the peroxisomes of the intermediate isopenicillin N and the precursors phenylacetic acid and coenzyme A. The mechanisms for the molecular transport of these precursors are still poorly understood. In this work, a search was made, in the genome of P. chrysogenum, in order to find a Major Facilitator Superfamily (MFS) membrane protein homologous to CefT of Acremonium chrysogenum, which is known to confer resistance to phenylacetic acid. The paaT gene was found to encode a MFS membrane protein containing 12 transmembrane spanners and one Pex19p-binding domain for Pex19-mediated targeting to peroxisomal membranes. RNA interference-mediated silencing of the paaT gene caused a clear reduction of benzylpenicillin secretion and increased the sensitivity of P. chrysogenum to the penicillin precursor phenylacetic acid. The opposite behavior was found when paaT was overexpressed from the glutamate dehydrogenase promoter that increases phenylacetic acid resistance and penicillin production. Localization studies by fluorescent laser scanning microscopy using PaaT-DsRed and EGFP-SKL fluorescent fusion proteins clearly showed that the protein was located in the peroxisomal membrane. The results suggested that PaaT is involved in penicillin production, most likely through the translocation of side-chain precursors (phenylacetic acid and phenoxyacetic acid) from the cytosol to the peroxisomal lumen across the peroxisomal membrane of P. chrysogenum.
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Affiliation(s)
- Marta Fernández-Aguado
- Area of Microbiology, Department of Molecular Biology, University of León, Campus de Vegazana s/n, 24071, León, Spain
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Qu P, Liu P, Fu P, Wang Y, Zhu W. [Secondary metabolites of halotolerant fungus Penicillium chrysogenum HK14-01 from the Yellow River Delta area]. Wei Sheng Wu Xue Bao 2012; 52:1103-1112. [PMID: 23236844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
OBJECTIVE To search for structurally novel and biologically active compounds from the secondary metabolites of halotolerant fungi from the Yellow River Delta area. METHODS We screened halotolerant fungi with rich chemical diversity and antitumor or antimicrobial activity by means of integrated chemical and biological method. We cultured halotolerant fungi under different conditions at first. Then we investigated the chemical diversity and the bioactivity of the EtOAc extracts of the fermentation broth by HPLC and TLC, and cytotoxic assay or antimicrobial assay. We selected Penicillium chrysogenum HK14-01 to further study for the large yield, producing alkaloids and cytotoxicity on P388 cells in YMDP culture medium containing 10% NaCl. We fermented P. chrysogenum HK14-01 on a large scale; we isolated and purified the compounds by column chromatography over silica gel, Sephadex LH-20, and semipreparative HPLC; and we identified the structures by spectroscopic analysis, X-ray diffraction (Mo-Kalpha), CD spectra and the time-dependent density functional theory electronic circular dichroism (TDDFT ECD) calculation. RESULTS We isolated and identified a halotolerant fungal strain, P. chrysogenum HK14-01, from the sediments collected in the Yellow River Delta area. From the fermentation broth of P. chrysogenum HK14-01, we isolated and identified eight compounds, i.e. (2S,3R)-oxaline (1, a major product), (3R, 4R)-3,4,8-trihydroxy-3,4-dihydronaphthalen-1 (2H)-one (2), (Z)-N-(4-hydroxy styryl) formamide (3), (E)-N-(4-hydroxystyryl) formamide (4), emodin (5), 4-(2-hydroxyethyl) benzene-1,2-diol (6), methyl 2-(4-hydroxyphenyl) acetate (7), and 2-(4-hydroxyphenyl) acetonitrile (8). CONCLUSION Bioactive compounds can be obtained from the secondary metabolites of halotolerant microorganisms from the Yellow River Delta area.
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Affiliation(s)
- Peng Qu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.
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Vargas-García MDC, López MJ, Suárez-Estrella F, Moreno J. Compost as a source of microbial isolates for the bioremediation of heavy metals: in vitro selection. Sci Total Environ 2012; 431:62-67. [PMID: 22664539 DOI: 10.1016/j.scitotenv.2012.05.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 05/03/2012] [Accepted: 05/03/2012] [Indexed: 05/27/2023]
Abstract
Heavy metal pollution has become a major environmental concern nowadays and the bioremediation of polluted habitats is an increasingly popular strategy due to both its efficiency and safety. A screening and selection protocol based on different composting processes was designed in order to isolate heavy metal-resistant microorganisms. A collection of 51 microorganisms was obtained and most of them showed the capability to tolerate heavy metals in multi-polluted aqueous systems (Cd(II), Cr(VI), Ni, Pb, Zn(II)), as well as to remove them. The highest detoxification ratios were observed for Pb. Some of the isolates detoxifying more than a 90% of this metal, while the other metals were removed in a range between 20% and 60%. The best isolates (Graphium putredinis, Fusarium solani, Fusarium sp. and Penicillium chrysogenum) were further assayed in order to determine the predominant removal mechanism and the potential use of their dead biomass as a biosorbent. Intracellular accumulation was the prevalent mechanism for most isolates and metals, with the exception of Ni. In this case, the proportion removed by extracellular adsorption was similar or even higher than that removed by intracellular accumulation. Thus, the efficiency of living cells was higher than that of dead biomass except in the case of Ni.
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Affiliation(s)
- María del Carmen Vargas-García
- Department of Applied Biology, Engineering Higher School, University of Almería-International Excellence Campus in Agri-Food, CeiA3, 04120 Almería, Spain.
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Veiga T, Nijland JG, Driessen AJM, Bovenberg RAL, Touw H, van den Berg MA, Pronk JT, Daran JM. Impact of velvet complex on transcriptome and penicillin G production in glucose-limited chemostat cultures of a β-lactam high-producing Penicillium chrysogenum strain. OMICS 2012; 16:320-33. [PMID: 22439693 PMCID: PMC3369278 DOI: 10.1089/omi.2011.0153] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The multicomponent global regulator Velvet complex has been identified as a key regulator of secondary metabolite production in Aspergillus and Penicillium species. Previous work indicated a massive impact of PcvelA and PclaeA deletions on penicillin production in prolonged batch cultures of P. chrysogenum, as well as substantial changes in transcriptome. The present study investigated the impact of these mutations on product formation and genome-wide transcript profiles under glucose-limited aerobic conditions, relevant for industrial production of β-lactams. Predicted amino acid sequences of PcVelA and PcLaeA in this strain were identical to those in its ancestor Wisconsin54-1255. Controls were performed to rule out transformation-associated loss of penicillin-biosynthesis clusters. The correct PcvelA and PclaeA deletion strains revealed a small reduction of penicillin G productivity relative to the reference strain, which is a much smaller reduction than previously reported for prolonged batch cultures of similar P. chrysogenum mutants. Chemostat-based transcriptome analysis yielded only 23 genes with a consistent differential response in the PcvelAΔ and PclaeAΔ mutants when grown in the absence of the penicillin G side-chain precursor phenylacetic acid. Eleven of these genes belonged to two small gene clusters, one of which contained a gene with high homology to the aristolochene synthase. These results provide a clear caveat that the impact of the Velvet complex on secondary metabolism in filamentous fungi is strongly context dependent.
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Affiliation(s)
- Tânia Veiga
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
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Opaliński Ł, Bartoszewska M, Fekken S, Liu H, de Boer R, van der Klei I, Veenhuis M, Kiel JAKW. De novo peroxisome biogenesis in Penicillium chrysogenum is not dependent on the Pex11 family members or Pex16. PLoS One 2012; 7:e35490. [PMID: 22536392 PMCID: PMC3334907 DOI: 10.1371/journal.pone.0035490] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 03/16/2012] [Indexed: 11/18/2022] Open
Abstract
We have analyzed the role of the three members of the Pex11 protein family in peroxisome formation in the filamentous fungus Penicillium chrysogenum. Two of these, Pex11 and Pex11C, are components of the peroxisomal membrane, while Pex11B is present at the endoplasmic reticulum. We show that Pex11 is a major factor involved in peroxisome proliferation. We also demonstrate that P. chrysogenum cells deleted for known peroxisome fission factors (all Pex11 family proteins and Vps1) still contain peroxisomes. Interestingly, we find that, unlike in mammals, Pex16 is not essential for peroxisome biogenesis in P. chrysogenum, as partially functional peroxisomes are present in a pex16 deletion strain. We also show that Pex16 is not involved in de novo biogenesis of peroxisomes, as peroxisomes were still present in quadruple Δpex11 Δpex11B Δpex11C Δpex16 mutant cells. By contrast, pex3 deletion in P. chrysogenum led to cells devoid of peroxisomes, suggesting that Pex3 may function independently of Pex16. Finally, we demonstrate that the presence of intact peroxisomes is important for the efficiency of ß-lactam antibiotics production by P. chrysogenum. Remarkably, distinct from earlier results with low penicillin producing laboratory strains, upregulation of peroxisome numbers in a high producing P. chrysogenum strain had no significant effect on penicillin production.
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Affiliation(s)
- Łukasz Opaliński
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kluyver Centre for Genomics of Industrial Fermentation, AG Groningen, the Netherlands
| | - Magdalena Bartoszewska
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kluyver Centre for Genomics of Industrial Fermentation, AG Groningen, the Netherlands
| | - Susan Fekken
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kluyver Centre for Genomics of Industrial Fermentation, AG Groningen, the Netherlands
| | - Haiyin Liu
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kluyver Centre for Genomics of Industrial Fermentation, AG Groningen, the Netherlands
| | - Rinse de Boer
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kluyver Centre for Genomics of Industrial Fermentation, AG Groningen, the Netherlands
| | - Ida van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kluyver Centre for Genomics of Industrial Fermentation, AG Groningen, the Netherlands
| | - Marten Veenhuis
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kluyver Centre for Genomics of Industrial Fermentation, AG Groningen, the Netherlands
| | - Jan A. K. W. Kiel
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kluyver Centre for Genomics of Industrial Fermentation, AG Groningen, the Netherlands
- * E-mail:
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Wolski EA, Barrera V, Castellari C, González JF. Biodegradation of phenol in static cultures by Penicillium chrysogenum ERK1: catalytic abilities and residual phytotoxicity. Rev Argent Microbiol 2012; 44:113-121. [PMID: 22997771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
Abstract
A phenol-degrading fungus was isolated from crop soils. Molecular characterization (using internal transcribed spacer, translation elongation factor and beta-tubulin gene sequences) and biochemical characterization allowed to identify the fungal strain as Penicillium chrysogenum Thom ERK1. Phenol degradation was tested at 25 degrees C under resting mycelium conditions at 6, 30, 60, 200, 350 and 400 mg/l of phenol as the only source of carbon and energy. The time required for complete phenol degradation increased at different initial phenol concentrations. Maximum specific degradation rate (0.89978 mg of phenol/day/mg of dry weight) was obtained at 200 mg/l. Biomass yield decreased at initial phenol concentrations above 60 mg/l. Catechol was identified as an intermediate metabolite by HPLC analysis and catechol dioxygenase activity was detected in plate assays, suggesting that phenol metabolism could occur via ortho fission of catechol. Wheat seeds were used as phytotoxicity indicators of phenol degradation products. It was found that these products were not phytotoxic for wheat but highly phytotoxic for phenol. The high specific degradation rates obtained under resting mycelium conditions are considered relevant for practical applications of this fungus in soil decontamination processes.
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Affiliation(s)
- Erika A Wolski
- Facultad de Ingeniería, Universidad Nacional de Mar del Plata, J. B. Justo 4302 (7600) Mar del Plata, Argentina.
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Koetsier MJ, Jekel PA, Wijma HJ, Bovenberg RAL, Janssen DB. Aminoacyl-coenzyme A synthesis catalyzed by a CoA ligase from Penicillium chrysogenum. FEBS Lett 2011; 585:893-8. [PMID: 21334330 DOI: 10.1016/j.febslet.2011.02.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2010] [Revised: 02/13/2011] [Accepted: 02/14/2011] [Indexed: 11/19/2022]
Abstract
Coenzyme A ligases play an important role in metabolism by catalyzing the activation of carboxylic acids. In this study we describe the synthesis of aminoacyl-coenzyme As (CoAs) catalyzed by a CoA ligase from Penicillium chrysogenum. The enzyme accepted medium-chain length fatty acids as the best substrates, but the proteinogenic amino acids L-phenylalanine and L-tyrosine, as well as the non-proteinogenic amino acids D-phenylalanine, D-tyrosine and (R)- and (S)-β-phenylalanine were also accepted. Of these amino acids, the highest activity was found for (R)-β-phenylalanine, forming (R)-β-phenylalanyl-CoA. Homology modeling suggested that alanine 312 is part of the active site cavity, and mutagenesis (A312G) yielded a variant that has an enhanced catalytic efficiency with β-phenylalanines and D-α-phenylalanine.
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Affiliation(s)
- Martijn J Koetsier
- Biochemical Laboratory, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen NL-9747 AG, The Netherlands
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Sigl C, Haas H, Specht T, Pfaller K, Kürnsteiner H, Zadra I. Among developmental regulators, StuA but not BrlA is essential for penicillin V production in Penicillium chrysogenum. Appl Environ Microbiol 2011; 77:972-82. [PMID: 21148688 PMCID: PMC3028705 DOI: 10.1128/aem.01557-10] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 12/02/2010] [Indexed: 11/20/2022] Open
Abstract
In filamentous fungi, secondary metabolism is often linked with developmental processes such as conidiation. In this study we analyzed the link between secondary metabolism and conidiation in the main industrial producer of the β-lactam antibiotic penicillin, the ascomycete Penicillium chrysogenum. Therefore, we generated mutants defective in two central regulators of conidiation, the transcription factors BrlA and StuA. Inactivation of either brlA or stuA blocked conidiation and altered hyphal morphology during growth on solid media, as shown by light and scanning electron microscopy, but did not affect biomass production during liquid-submerged growth. Genome-wide transcriptional profiling identified a complex StuA- and BrlA-dependent regulatory network, including genes previously shown to be involved in development and secondary metabolism. Remarkably, inactivation of stuA, but not brlA, drastically downregulated expression of the penicillin biosynthetic gene cluster during solid and liquid-submerged growth. In agreement, penicillin V production was wild-type-like in brlA-deficient strains but 99% decreased in stuA-deficient strains during liquid-submerged growth, as shown by high-performance liquid chromatography (HPLC) analysis. Thus, among identified regulators of penicillin V production StuA has the most severe influence. Overexpression of stuA increased the transcript levels of brlA and abaA (another developmental regulator) and derepressed conidiation during liquid-submerged growth but did not affect penicillin V productivity. Taken together, these data demonstrate an intimate but not exclusive link between regulation of development and secondary metabolism in P. chrysogenum.
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Affiliation(s)
- Claudia Sigl
- Anti Infectives Microbiology, Sandoz GmbH, Biochemiestrasse 10, 6250 Kundl, Austria, Christian Doppler Laboratory for Fungal Biotechnology, Biocenter, Division of Molecular Biology, Innsbruck Medical University, Fritz-Pregl-Strasse 3, 6020 Innsbruck, Austria, Division of Histology and Embryology, Department of Anatomy, Histology and Embryology, Innsbruck Medical University, Müllerstrasse 59, 6020 Innsbruck, Austria
| | - Hubertus Haas
- Anti Infectives Microbiology, Sandoz GmbH, Biochemiestrasse 10, 6250 Kundl, Austria, Christian Doppler Laboratory for Fungal Biotechnology, Biocenter, Division of Molecular Biology, Innsbruck Medical University, Fritz-Pregl-Strasse 3, 6020 Innsbruck, Austria, Division of Histology and Embryology, Department of Anatomy, Histology and Embryology, Innsbruck Medical University, Müllerstrasse 59, 6020 Innsbruck, Austria
| | - Thomas Specht
- Anti Infectives Microbiology, Sandoz GmbH, Biochemiestrasse 10, 6250 Kundl, Austria, Christian Doppler Laboratory for Fungal Biotechnology, Biocenter, Division of Molecular Biology, Innsbruck Medical University, Fritz-Pregl-Strasse 3, 6020 Innsbruck, Austria, Division of Histology and Embryology, Department of Anatomy, Histology and Embryology, Innsbruck Medical University, Müllerstrasse 59, 6020 Innsbruck, Austria
| | - Kristian Pfaller
- Anti Infectives Microbiology, Sandoz GmbH, Biochemiestrasse 10, 6250 Kundl, Austria, Christian Doppler Laboratory for Fungal Biotechnology, Biocenter, Division of Molecular Biology, Innsbruck Medical University, Fritz-Pregl-Strasse 3, 6020 Innsbruck, Austria, Division of Histology and Embryology, Department of Anatomy, Histology and Embryology, Innsbruck Medical University, Müllerstrasse 59, 6020 Innsbruck, Austria
| | - Hubert Kürnsteiner
- Anti Infectives Microbiology, Sandoz GmbH, Biochemiestrasse 10, 6250 Kundl, Austria, Christian Doppler Laboratory for Fungal Biotechnology, Biocenter, Division of Molecular Biology, Innsbruck Medical University, Fritz-Pregl-Strasse 3, 6020 Innsbruck, Austria, Division of Histology and Embryology, Department of Anatomy, Histology and Embryology, Innsbruck Medical University, Müllerstrasse 59, 6020 Innsbruck, Austria
| | - Ivo Zadra
- Anti Infectives Microbiology, Sandoz GmbH, Biochemiestrasse 10, 6250 Kundl, Austria, Christian Doppler Laboratory for Fungal Biotechnology, Biocenter, Division of Molecular Biology, Innsbruck Medical University, Fritz-Pregl-Strasse 3, 6020 Innsbruck, Austria, Division of Histology and Embryology, Department of Anatomy, Histology and Embryology, Innsbruck Medical University, Müllerstrasse 59, 6020 Innsbruck, Austria
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Zhao Z, Kuijvenhoven K, van Gulik WM, Heijnen JJ, van Winden WA, Verheijen PJT. Cytosolic NADPH balancing in Penicillium chrysogenum cultivated on mixtures of glucose and ethanol. Appl Microbiol Biotechnol 2011; 89:63-72. [PMID: 20809073 PMCID: PMC3016204 DOI: 10.1007/s00253-010-2851-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 08/09/2010] [Accepted: 08/16/2010] [Indexed: 11/02/2022]
Abstract
The in vivo flux through the oxidative branch of the pentose phosphate pathway (oxPPP) in Penicillium chrysogenum was determined during growth in glucose/ethanol carbon-limited chemostat cultures, at the same growth rate. Non-stationary (13)C flux analysis was used to measure the oxPPP flux. A nearly constant oxPPP flux was found for all glucose/ethanol ratios studied. This indicates that the cytosolic NADPH supply is independent of the amount of assimilated ethanol. The cofactor assignment in the model of van Gulik et al. (Biotechnol Bioeng 68(6):602-618, 2000) was supported using the published genome annotation of P. chrysogenum. Metabolic flux analysis showed that NADPH requirements in the cytosol remain nearly the same in these experiments due to constant biomass growth. Based on the cytosolic NADPH balance, it is known that the cytosolic aldehyde dehydrogenase in P. chrysogenum is NAD(+) dependent. Metabolic modeling shows that changing the NAD(+)-aldehyde dehydrogenase to NADP(+)-aldehyde dehydrogenase can increase the penicillin yield on substrate.
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Affiliation(s)
- Zheng Zhao
- Department of Biotechnology, Kluyver Centre for Genomics of Industrial Fermentation, Delft University of Technology, Julianalaan 67, 2628BC Delft, The Netherlands
| | - Karel Kuijvenhoven
- Department of Biotechnology, Kluyver Centre for Genomics of Industrial Fermentation, Delft University of Technology, Julianalaan 67, 2628BC Delft, The Netherlands
| | - Walter M. van Gulik
- Department of Biotechnology, Kluyver Centre for Genomics of Industrial Fermentation, Delft University of Technology, Julianalaan 67, 2628BC Delft, The Netherlands
| | - Joseph J. Heijnen
- Department of Biotechnology, Kluyver Centre for Genomics of Industrial Fermentation, Delft University of Technology, Julianalaan 67, 2628BC Delft, The Netherlands
| | | | - Peter J. T. Verheijen
- Department of Biotechnology, Kluyver Centre for Genomics of Industrial Fermentation, Delft University of Technology, Julianalaan 67, 2628BC Delft, The Netherlands
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Gao SS, Li XM, Du FY, Li CS, Proksch P, Wang BG. Secondary metabolites from a marine-derived endophytic fungus Penicillium chrysogenum QEN-24S. Mar Drugs 2010; 9:59-70. [PMID: 21339945 PMCID: PMC3039470 DOI: 10.3390/md9010059] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 12/01/2010] [Accepted: 12/20/2010] [Indexed: 11/16/2022] Open
Abstract
Penicillium chrysogenum QEN-24S, an endophytic fungus isolated from an unidentified marine red algal species of the genus Laurencia, displayed inhibitory activity against the growth of pathogen Alternaria brassicae in dual culture test. Chemical investigation of this fungal strain resulted in the isolation of four new (1–3 and 5) and one known (4) secondary metabolites. Their structures were identified as two polyketide derivatives penicitides A and B (1 and 2), two glycerol derivatives 2-(2,4-dihydroxy-6-methylbenzoyl)-glycerol (3) and 1-(2,4-dihydroxy-6-methylbenzoyl)- glycerol (4), and one monoterpene derivative penicimonoterpene (5). Penicitides A and B (1 and 2) feature a unique 10-hydroxy- or 7,10-dihydroxy-5,7-dimethylundecyl moiety substituting at C-5 of the α-tetrahydropyrone ring, which is not reported previously among natural products. Compound 5 displayed potent activity against the pathogen A. brassicae, while compound 1 exhibited moderate cytotoxic activity against the human hepatocellular liver carcinoma cell line.
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Affiliation(s)
- Shu-Shan Gao
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China; E-Mails: (S.-S.G.); (X.-M.L.); (F.-Y.D.); (C.-S.L.)
- Graduate School of the Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
| | - Xiao-Ming Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China; E-Mails: (S.-S.G.); (X.-M.L.); (F.-Y.D.); (C.-S.L.)
| | - Feng-Yu Du
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China; E-Mails: (S.-S.G.); (X.-M.L.); (F.-Y.D.); (C.-S.L.)
| | - Chun-Shun Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China; E-Mails: (S.-S.G.); (X.-M.L.); (F.-Y.D.); (C.-S.L.)
| | - Peter Proksch
- Institute for Pharmaceutical Biology and Biotechnology, Heinrich-Heine-University Duesseldorf, Universitaetsstreet 1, 40225 Duesseldorf, Germany; E-Mail:
| | - Bin-Gui Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Nanhai Road 7, Qingdao 266071, China; E-Mails: (S.-S.G.); (X.-M.L.); (F.-Y.D.); (C.-S.L.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel./Fax: +86-532-82898553
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García-Rico RO, Martín JF, Fierro F. Heterotrimeric Gα protein Pga1 from Penicillium chrysogenum triggers germination in response to carbon sources and affects negatively resistance to different stress conditions. Fungal Genet Biol 2010; 48:641-9. [PMID: 21146624 DOI: 10.1016/j.fgb.2010.11.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2010] [Revised: 11/15/2010] [Accepted: 11/30/2010] [Indexed: 11/19/2022]
Abstract
Heterotrimeric Gα protein Pga1 of Penicillium chrysogenum controls vegetative growth, conidiation and secondary metabolite production. In this work we studied the role of Pga1 in spore germination and resistance to different stress conditions. Strains G203R-T (expressing the dominant inactivating pga1(G203R) allele) and Δpga1 (deleted pga1) showed a delayed and asynchronic germination pattern, and a decrease in the percentage of germination, which occurred in only 70-80% of the total conidia. In contrast, in strains expressing the dominant activating pga1(G42R) allele, germination occurred at earlier times and in 100% of conidia. In addition, strains with the pga1(G42R) allele were able to bypass the carbon source (glucose or sucrose) requirement for germination in about 64% of conidia. Thus Pga1 plays an important, but not essential, role in germination, mediating carbon source sensing. Regulation of germination by Pga1 is probably mediated by cAMP, as intracellular levels of this secondary messenger undergo a peak before the onset of germination only in strains with an active Pga1. Pga1 activity is also a determinant factor in the resistance to different stress conditions. Absence or inactivation of Pga1 allow growth on SDS-containing minimal medium, increase resistance of conidia to thermal and oxidative stress, and increase resistance of vegetative mycelium to thermal and osmotic stress. In contrast, constitutive activation of Pga1 causes a decrease in the resistance of conidia to thermal stress and of vegetative mycelium to thermal and osmotic stress. Together with our previously reported results, we show in this work that Pga1 plays a central role in the regulation of the whole growth-developmental program of this biotechnologically important fungus.
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Affiliation(s)
- Ramón Ovidio García-Rico
- Institute of Biotechnology of León (INBIOTEC), Parque Científico de León, Av. Real 1, 24006 León, Spain.
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Jami MS, Barreiro C, García-Estrada C, Martín JF. Proteome analysis of the penicillin producer Penicillium chrysogenum: characterization of protein changes during the industrial strain improvement. Mol Cell Proteomics 2010; 9:1182-98. [PMID: 20154335 PMCID: PMC2877979 DOI: 10.1074/mcp.m900327-mcp200] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 01/15/2010] [Indexed: 11/06/2022] Open
Abstract
Proteomics is a powerful tool to understand the molecular mechanisms causing the production of high penicillin titers by industrial strains of the filamentous fungus Penicillium chrysogenum as the result of strain improvement programs. Penicillin biosynthesis is an excellent model system for many other bioactive microbial metabolites. The recent publication of the P. chrysogenum genome has established the basis to understand the molecular processes underlying penicillin overproduction. We report here the proteome reference map of P. chrysogenum Wisconsin 54-1255 (the genome project reference strain) together with an in-depth study of the changes produced in three different strains of this filamentous fungus during industrial strain improvement. Two-dimensional gel electrophoresis, peptide mass fingerprinting, and tandem mass spectrometry were used for protein identification. Around 1000 spots were visualized by "blue silver" colloidal Coomassie staining in a non-linear pI range from 3 to 10 with high resolution, which allowed the identification of 950 proteins (549 different proteins and isoforms). Comparison among the cytosolic proteomes of the wild-type NRRL 1951, Wisconsin 54-1255 (an improved, moderate penicillin producer), and AS-P-78 (a penicillin high producer) strains indicated that global metabolic reorganizations occurred during the strain improvement program. The main changes observed in the high producer strains were increases of cysteine biosynthesis (a penicillin precursor), enzymes of the pentose phosphate pathway, and stress response proteins together with a reduction in virulence and in the biosynthesis of other secondary metabolites different from penicillin (pigments and isoflavonoids). In the wild-type strain, we identified enzymes to utilize cellulose, sorbitol, and other carbon sources that have been lost in the high penicillin producer strains. Changes in the levels of a few specific proteins correlated well with the improved penicillin biosynthesis in the high producer strains. These results provide useful information to improve the production of many other bioactive secondary metabolites.
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Affiliation(s)
- Mohammad-Saeid Jami
- From the ‡Área de Microbiología, Departamento de Biología Molecular, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain and
| | - Carlos Barreiro
- ¶INBIOTEC, Instituto de Biotecnología de León, Avenida Real No. 1, Parque Científico de León, 24006 León, Spain
| | - Carlos García-Estrada
- ¶INBIOTEC, Instituto de Biotecnología de León, Avenida Real No. 1, Parque Científico de León, 24006 León, Spain
| | - Juan-Francisco Martín
- From the ‡Área de Microbiología, Departamento de Biología Molecular, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain and
- ¶INBIOTEC, Instituto de Biotecnología de León, Avenida Real No. 1, Parque Científico de León, 24006 León, Spain
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Smidák R, Jopcík M, Kralovicová M, Gajdosíková J, Kormanec J, Timko J, Turna J. Core promoters of the penicillin biosynthesis genes and quantitative RT-PCR analysis of these genes in high and low production strain of Penicillium chrysogenum. Folia Microbiol (Praha) 2010; 55:126-32. [PMID: 20490754 DOI: 10.1007/s12223-010-0019-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Revised: 12/09/2009] [Indexed: 11/30/2022]
Abstract
The transcription start points of the penicillin biosynthesis genes from Penicillium chrysogenum were mapped using the primer extension method. For each of the three genes consensus sequences of the core promoter elements were identified, supporting the notion that the basal transcription of these genes is mediated separately. Interestingly, transcription start of the pcbC gene is located within the potential Inr element with no TATA box-like sequence being found at expected position. This is in contrast to pcbAB and penDE genes with proposed TATA boxes or even to Aspergillus nidulans ipnA (pcbC) gene indicating possible differences in basal transcription regulation. Using the quantitative RT-PCR analysis the expression of all three biosynthesis genes was monitored in both the high and low production strain of P. chrysogenum during a 3-d cultivation under production conditions. The differences were found between the strains in time regulation and transcript levels of the biosynthesis genes. Furthermore, we showed that the effect of higher gene dosage on productivity in the production strain is amplified by more efficient transcription of the biosynthesis genes with the RNA levels approximately 37- and 12-times higher, respectively, than in a low production strain.
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Affiliation(s)
- R Smidák
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51, Bratislava 45, Slovak Republic.
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Rodríguez-Martín A, Acosta R, Liddell S, Núñez F, Benito MJ, Asensio MA. Characterization of the novel antifungal protein PgAFP and the encoding gene of Penicillium chrysogenum. Peptides 2010; 31:541-7. [PMID: 19914321 DOI: 10.1016/j.peptides.2009.11.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Revised: 11/04/2009] [Accepted: 11/04/2009] [Indexed: 11/24/2022]
Abstract
The strain RP42C from Penicillium chrysogenum produces a small protein PgAFP that inhibits the growth of some toxigenic molds. The molecular mass of the protein determined by electrospray ionization mass spectrometry (ESI-MS) was 6 494Da. PgAFP showed a cationic character with an estimated pI value of 9.22. Upon chemical and enzymatic treatments of PgAFP, no evidence for N- or O-glycosylations was obtained. Five partial sequences of PgAFP were obtained by Edman degradation and by ESI-MS/MS after trypsin and chymotrypsin digestions. Using degenerate primers from these peptide sequences, a segment of 70bp was amplified by PCR from pgafp gene. 5'- and 3'-ends of pgafp were obtained by RACE-PCR with gene-specific primers designed from the 70bp segment. The complete pgafp sequence of 404bp was obtained using primers designed from 5'- and 3'-ends. Comparison of genomic and cDNA sequences revealed a 279bp coding region interrupted by two introns of 63 and 62bp. The precursor of the antifungal protein consists of 92 amino acids and appears to be processed to the mature 58 amino acids PgAFP. The deduced amino acid sequence of the mature protein shares 79% identity to the antifungal protein Anafp from Aspergillus niger. PgAFP is a new protein that belongs to the group of small, cysteine-rich, and basic proteins with antifungal activity produced by ascomycetes. Given that P. chrysogenum is regarded as safe mold commonly found in foods, PgAFP may be useful to prevent growth of toxigenic molds in food and agricultural products.
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Affiliation(s)
- Andrea Rodríguez-Martín
- Higiene y Seguridad Alimentaria, Facultad de Veterinaria, Universidad de Extremadura, Avda. de la Universidad, 10071 Cáceres, Spain
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Yang J, An Y, Xu X, Liu G. [Effects of Pa-pex 11 gene on penicillin production in Penicillium aurantiogriseum]. Wei Sheng Wu Xue Bao 2009; 49:1477-1482. [PMID: 20112676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
OBJECTIVE To study the effect of Pa-pex 11 gene on penicillin production in Pencillium aurantiogriseum. METHOD Based on the conserved domain of pex 11 from Penicillium chrysogenum, we designed primers pex01 and pex02 to amplify Pa-pex 11 gene from P. aurantiogriseum. The complete Pa-pex 11 gene was cloned via thermal asymmetric interlaced PCR (Tail-PCR). In order to obtain tranformants with additional Pa-pex 11 gene copy, ATMT (Agrobacterium tumefaciens mediated transformation) was used to transform P. aurantiogriseum. The copy number of Pa-pex 11 was measured by quantitative PCR. Penicillin production of the transformant was analyzed by bioassays and the microbodies were observed by transmission electron microscope (TEM). RESULTS ATMT was successfully applied in P. aurantiogriseum. Increasing the copy number of Pa-pex 11 gene resulted in a 1.7-fold increase of pencillin production, and the electron microscope graph showed that the number of microbodies increased obviously. CONCLUSION Our results suggest that increasing the copy number of Pa-pex 11 can increase the number of microbodies, and stimulate the penicillin production.
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Affiliation(s)
- Jing Yang
- Key Laboratory Systematic Mycology and Lichenology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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Yamamoto N, Matsuzaka Y, Kimura M, Matsuki H, Yanagisawa Y. Comparison of dry- and wet-based fine bead homogenizations to extract DNA from fungal spores. J Biosci Bioeng 2009; 107:464-70. [PMID: 19332310 DOI: 10.1016/j.jbiosc.2008.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Revised: 11/05/2008] [Accepted: 12/06/2008] [Indexed: 11/19/2022]
Abstract
The present study explored DNA extraction kinetics from fungal spores, i.e., Aspergillus niger, Penicillium chrysogenum and Cladosporium sphaerospermum, by fine bead mill homogenization. In particular, the study aimed to investigate basic differences between the dry- and wet-based methods. The results showed higher initial rates of the DNA extractions by the dry-based method than by the wet-based method, due to higher collision efficiency among fine beads and fungal spores. Based on the experimental results, we constructed kinetic models. While the results by the wet-based method were fitted well with an existing first-order release-degradation model, the results by the dry-based method were not fitted well. Meanwhile, a newly constructed first-order release-degradation model, assuming a proportion of the DNA remained inside the disrupted spore cells and protected from further sheer stress, showed good correlations. The real-time PCR assays showed the PCR efficiencies of the DNA obtained by the dry-based method were higher than those by the wet-based method likely due to increased moderate fragmentation of the DNA by the dry-based method. Thus, although wet-based methods have been commonly used, dry-based methods might also be applicable to achieve efficient extraction and PCR amplification of fungal DNA.
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Affiliation(s)
- Naomichi Yamamoto
- Department of Nursing, School of Health Sciences, Tokai University, Bohseidai, Isehara-shi, Kanagawa, Japan.
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Harris DM, van der Krogt ZA, Klaassen P, Raamsdonk LM, Hage S, van den Berg MA, Bovenberg RAL, Pronk JT, Daran JM. Exploring and dissecting genome-wide gene expression responses of Penicillium chrysogenum to phenylacetic acid consumption and penicillinG production. BMC Genomics 2009; 10:75. [PMID: 19203396 PMCID: PMC2657799 DOI: 10.1186/1471-2164-10-75] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Accepted: 02/10/2009] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Since the discovery of the antibacterial activity of penicillin by Fleming 80 years ago, improvements of penicillin titer were essentially achieved by classical strain improvement through mutagenesis and screening. The recent sequencing of Penicillium chrysogenum strain Wisconsin1255-54 and the availability of genomics tools such as DNA-microarray offer new perspective. RESULTS In studies on beta-lactam production by P. chrysogenum, addition and omission of a side-chain precursor is commonly used to generate producing and non-producing scenarios. To dissect effects of penicillinG production and of its side-chain precursor phenylacetic acid (PAA), a derivative of a penicillinG high-producing strain without a functional penicillin-biosynthesis gene cluster was constructed. In glucose-limited chemostat cultures of the high-producing and cluster-free strains, PAA addition caused a small reduction of the biomass yield, consistent with PAA acting as a weak-organic-acid uncoupler. Microarray-based analysis on chemostat cultures of the high-producing and cluster-free strains, grown in the presence and absence of PAA, showed that: (i) Absence of a penicillin gene cluster resulted in transcriptional upregulation of a gene cluster putatively involved in production of the secondary metabolite aristolochene and its derivatives, (ii) The homogentisate pathway for PAA catabolism is strongly transcriptionally upregulated in PAA-supplemented cultures (iii) Several genes involved in nitrogen and sulfur metabolism were transcriptionally upregulated under penicillinG producing conditions only, suggesting a drain of amino-acid precursor pools. Furthermore, the number of candidate genes for penicillin transporters was strongly reduced, thus enabling a focusing of functional analysis studies. CONCLUSION This study demonstrates the usefulness of combinatorial transcriptome analysis in chemostat cultures to dissect effects of biological and process parameters on gene expression regulation. This study provides for the first time clear-cut target genes for metabolic engineering, beyond the three genes of the beta-lactam pathway.
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Affiliation(s)
- Diana M Harris
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Zita A van der Krogt
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Paul Klaassen
- DSM Anti-Infectives, DAI/INNO (624-0270), Postbus 425, 2600 AK, Delft, The Netherlands
| | - Leonie M Raamsdonk
- DSM Anti-Infectives, DAI/INNO (624-0270), Postbus 425, 2600 AK, Delft, The Netherlands
| | - Susanne Hage
- DSM Anti-Infectives, DAI/INNO (624-0270), Postbus 425, 2600 AK, Delft, The Netherlands
| | - Marco A van den Berg
- DSM Anti-Infectives, DAI/INNO (624-0270), Postbus 425, 2600 AK, Delft, The Netherlands
| | - Roel AL Bovenberg
- DSM Anti-Infectives, DAI/INNO (624-0270), Postbus 425, 2600 AK, Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands
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Thykaer J, Rueksomtawin K, Noorman H, Nielsen J. Disruption of the NADPH-dependent glutamate dehydrogenase affects the morphology of two industrial strains of Penicillium chrysogenum. J Biotechnol 2009; 139:280-2. [PMID: 19167440 DOI: 10.1016/j.jbiotec.2008.12.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Revised: 09/09/2008] [Accepted: 12/18/2008] [Indexed: 11/18/2022]
Abstract
New morphological aspects of Penicillium chrysogenum were found during physiological characterisation of two NADPH-dependent glutamate dehydrogenase mutant strains. A morphological characterisation of the previously constructed strains, together with the two beta-lactam producing industrial recipient strains, was conducted. The reference strains showed a compact structure with highly branched hyphal elements whereas the morphology of the DeltagdhA strains consisting of long elongated hyphal elements with few branches. On solid medium, the hyphal growth unit (length) increased from an average of 47 microm tip(-1) in the reference strains to 117 microm tip(-1) in the DeltagdhA strains and in submerged cultures a decrease of 18% in branching frequency was measured due to the gdhA deletion. P. chrysogenum Wis 54-1255, the ancestor of most production strains was also characterised and this strain showed morphology similar to the industrial strains. Interestingly, the constructed strains showed morphology similar to wild type Aspergillus nidulans another species carrying the penicillin biosynthetic cluster. Thus, the results showed that elimination of glutamate dehydrogenase activity in high producing strains of P. chrysogenum has a radical impact on morphology.
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Affiliation(s)
- Jette Thykaer
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, Building 223, DK-2800 Kgs., Lyngby, Denmark
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Omura F, Hatanaka H, Nakao Y. Characterization of a novel tyrosine permease of lager brewing yeast shared by Saccharomyces cerevisiae strain RM11-1a. FEMS Yeast Res 2007; 7:1350-61. [PMID: 17825063 DOI: 10.1111/j.1567-1364.2007.00310.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
In Saccharomyces cerevisiae yeast, the uptake of aromatic amino acids is mediated by the relatively specific permeases Tat1p, Tat2p, Bap2p, and Bap3p, as well as by two other permeases with broader specificities: Gap1p and Agp1p. Here, a novel permease gene TAT3 (Tyrosine Amino acid Transporter) identified in the S. cerevisiae-type subset genome of the lager brewing yeast strain Weihenstephan Nr.34 (34/70) is reported. The TAT3 sequence was also found in the genome of S. cerevisiae strain RM11-1a, but not in S. cerevisiae strain S288C. Tat3p showed a significant similarity to Penicillium chrysogenum ArlP permease, which has transport activity for aromatic amino acids and leucine. When overexpressed in ssy1Delta gap1Delta mutant cells, Tat3p exhibited a tyrosine transport activity with an apparent K(m) of 160 microM. TAT3 transcription in lager brewing yeast was subjected to nitrogen catabolite repression in a manner similar to that of GAP1. Furthermore, the subcellular localization of Tat3p-green fluorescent protein (GFP) fusion protein was dependent on the quality of the nitrogen source, indicating a post-translational control of Tat3p function.
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Affiliation(s)
- Fumihiko Omura
- Suntory Research Center, Shimamoto-cho, Mishima-gun, Osaka, Japan.
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van den Berg MA, Westerlaken I, Leeflang C, Kerkman R, Bovenberg RAL. Functional characterization of the penicillin biosynthetic gene cluster of Penicillium chrysogenum Wisconsin54-1255. Fungal Genet Biol 2007; 44:830-44. [PMID: 17548217 DOI: 10.1016/j.fgb.2007.03.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Revised: 03/17/2007] [Accepted: 03/23/2007] [Indexed: 11/28/2022]
Abstract
Industrial strain improvement via classical mutagenesis is a black box approach. In an attempt to learn from and understand the mutations introduced, we cloned and characterized the amplified region of industrial penicillin production strains. Upon amplification of this region Penicillium chrysogenum is capable of producing an increased amount of antibiotics, as was previously reported [Barredo, J.L., Diez, B., Alvarez, E., Martín, J.F., 1989a. Large amplification of a 35-kb DNA fragment carrying two penicillin biosynthetic genes in high yielding strains of Penicillium chrysogenum. Curr. Genet. 16, 453-459; Newbert, R.W., Barton, B., Greaves, P., Harper, J., Turner, G., 1997. Analysis of a commercially improved Penicillium chrysogenum strain series, involvement of recombinogenic regions in amplification and deletion of the penicillin gene cluster. J. Ind. Microbiol. 19, 18-27]. Bioinformatic analysis of the central 56.9kb, present as six direct repeats in the strains analyzed in this study, predicted 15 Open Reading Frames (ORFs). Besides the three penicillin biosynthetic genes (pcbAB, pcbC and penDE) only one ORF has an orthologue of known function in the database: the Saccharomyces cerevisiae gene ERG25. Surprisingly, many genes known to encode direct or indirect steps beta-lactam biosynthesis like phenyl acetic acid CoA ligase and transporters are not present. Detailed analyses reveal a detectable transcript for most of the predicted ORFs under the conditions tested. We have studied the role of these in relation to penicillin production and amplification of the biosynthetic gene cluster. In contrast to what was expected, the genes encoding the three penicillin biosynthetic enzymes alone are sufficient to restore full beta-lactam synthesis in a mutant lacking the complete region. Therefore, the role of the other 12 ORFs in this region seems irrelevant for penicillin biosynthesis.
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Affiliation(s)
- Marco A van den Berg
- DSM Anti-Infectives, DSM Gist (624-0270), P.O. Box 425, 2600 AK, Delft, The Netherlands.
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