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Nie H, Zhang Y, Li M, Wang W, Wang Z, Zheng J. Expression of microbial lipase in filamentous fungus Aspergillus niger: a review. 3 Biotech 2024; 14:172. [PMID: 38841267 PMCID: PMC11147998 DOI: 10.1007/s13205-024-03998-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/28/2024] [Indexed: 06/07/2024] Open
Abstract
Lipase has high economic importance and is widely used in biodiesel, food, detergents, cosmetics, and pharmaceutical industries. The rapid development of synthetic biology and system biology has not only paved the way for comprehensively understanding the efficient operation mechanism of Aspergillus niger cell factories but also introduced a new technological system for creating and optimizing high-efficiency A. niger cell factories. In this review, all relevant data on microbial lipase enzyme sources and general properties are gathered and updated. The relationship between A. niger strain morphology and protein production is discussed. The safety of A. niger strain is investigated to ensure product safety. The biotechnologies and factors influencing lipase expression in A. niger are summarized. This review focuses on various strategies to improve lipase expression in A. niger. The summary of these methods and the application of the gene editing technology CRISPR/Cas9 system can further improve the efficiency of constructing the engineered lipase-producing A. niger.
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Affiliation(s)
- Hongmei Nie
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
| | - Yueting Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
| | - Mengjiao Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
| | - Weili Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
| | - Zhao Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
| | - Jianyong Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
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2
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Barreiro C, Albillos SM, García-Estrada C. Penicillium chrysogenum: Beyond the penicillin. ADVANCES IN APPLIED MICROBIOLOGY 2024; 127:143-221. [PMID: 38763527 DOI: 10.1016/bs.aambs.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
Almost one century after the Sir Alexander Fleming's fortuitous discovery of penicillin and the identification of the fungal producer as Penicillium notatum, later Penicillium chrysogenum (currently reidentified as Penicillium rubens), the molecular mechanisms behind the massive production of penicillin titers by industrial strains could be considered almost fully characterized. However, this filamentous fungus is not only circumscribed to penicillin, and instead, it seems to be full of surprises, thereby producing important metabolites and providing expanded biotechnological applications. This review, in addition to summarizing the classical role of P. chrysogenum as penicillin producer, highlights its ability to generate an array of additional bioactive secondary metabolites and enzymes, together with the use of this microorganism in relevant biotechnological processes, such as bioremediation, biocontrol, production of bioactive nanoparticles and compounds with pharmaceutical interest, revalorization of agricultural and food-derived wastes or the enhancement of food industrial processes and the agricultural production.
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Affiliation(s)
- Carlos Barreiro
- Área de Bioquímica y Biología Molecular, Departamento de Biología Molecular, Facultad de Veterinaria, Universidad de León, León, Spain; Instituto de Biología Molecular, Genómica y Proteómica (INBIOMIC), Universidad de León, León, Spain.
| | - Silvia M Albillos
- Área de Bioquímica y Biología Molecular, Departamento de Biotecnología y Ciencia de los Alimentos, Facultad de Ciencias, Universidad de Burgos, Burgos, Spain
| | - Carlos García-Estrada
- Departamento de Ciencias Biomédicas, Facultad de Veterinaria, Universidad de León, León, Spain; Instituto de Biomedicina (IBIOMED), Universidad de León, León, Spain
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3
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Sawant AM, Navale VD, Vamkudoth KR. Isolation and Molecular Characterization of Indigenous Penicillium chrysogenum/ rubens Strain Portfolio for Penicillin V Production. Microorganisms 2023; 11:1132. [PMID: 37317105 DOI: 10.3390/microorganisms11051132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/29/2023] [Accepted: 04/10/2023] [Indexed: 06/16/2023] Open
Abstract
Beta (β)-lactam antibiotic is an industrially important molecule produced by Penicillium chrysogenum/rubens. Penicillin is a building block for 6-aminopenicillanic acid (6-APA), an important active pharmaceutical intermediate (API) used for semi-synthetic antibiotics biosynthesis. In this investigation, we isolated and identified Penicillium chrysogenum, P. rubens, P. brocae, P. citrinum, Aspergillus fumigatus, A. sydowii, Talaromyces tratensis, Scopulariopsis brevicaulis, P. oxalicum, and P. dipodomyicola using the internal transcribed spacer (ITS) region and the β-tubulin (BenA) gene for precise species identification from Indian origin. Furthermore, the BenA gene distinguished between complex species of P. chrysogenum and P. rubens to a certain extent which partially failed by the ITS region. In addition, these species were distinguished by metabolic markers profiled by liquid chromatography-high resolution mass spectrometry (LC-HRMS). Secalonic acid, Meleagrin, and Roquefortine C were absent in P. rubens. The crude extract evaluated for PenV production by antibacterial activities by well diffusion method against Staphylococcus aureus NCIM-2079. A high-performance liquid chromatography (HPLC) method was developed for simultaneous detection of 6-APA, phenoxymethyl penicillin (PenV), and phenoxyacetic acid (POA). The pivotal objective was the development of an indigenous strain portfolio for PenV production. Here, a library of 80 strains of P. chrysogenum/rubens was screened for PenV production. Results showed 28 strains capable of producing PenV in a range from 10 to 120 mg/L when 80 strains were screened for its production. In addition, fermentation parameters, precursor concentration, incubation period, inoculum size, pH, and temperature were monitored for the improved PenV production using promising P. rubens strain BIONCL P45. In conclusion, P. chrysogenum/rubens strains can be explored for the industrial-scale PenV production.
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Affiliation(s)
- Amol M Sawant
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Vishwambar D Navale
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Koteswara Rao Vamkudoth
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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4
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Umemura M, Tamano K. How to improve the production of peptidyl compounds in filamentous fungi. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:1085624. [PMID: 37746201 PMCID: PMC10512285 DOI: 10.3389/ffunb.2022.1085624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/02/2022] [Indexed: 09/26/2023]
Abstract
Peptidyl compounds produced by filamentous fungi, which are nonribosomal peptides (NRPs) and ribosomally synthesized and post-translationally modified peptides (RiPPs), are rich sources of bioactive compounds with a wide variety of structures. Some of these peptidyl compounds are useful as pharmaceuticals and pesticides. However, for industrial use, their low production often becomes an obstacle, and various approaches have been challenged to overcome this weakness. In this article, we summarize the successful attempts to increase the production of NRPs and RiPPs in filamentous fungi and present our perspectives on how to improve it further.
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Affiliation(s)
- Maiko Umemura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Koichi Tamano
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
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Huang Y, Zou K, Qing T, Feng B, Zhang P. Metagenomics and metatranscriptomics analyses of antibiotic synthesis in activated sludge. ENVIRONMENTAL RESEARCH 2022; 213:113741. [PMID: 35750126 DOI: 10.1016/j.envres.2022.113741] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/23/2022] [Accepted: 06/18/2022] [Indexed: 06/15/2023]
Abstract
The generic of antibiotics is considered to be a main reason for the generation of antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs). However, little has been reported about the antibiotic biosynthesis by activated sludge. In this study, the distribution and expression of antibiotic biosynthetic genes (ABGs) in the floc sludge and biofilm from two WWTPs were deciphered using metagenomics and metatranscriptomics. The results showed that 2% of the community were in general well-linked to antibiotic production, indicating a non-negligible antibiotic synthetic ability of WWTPs. 93 ABGs belonging to 26 antibiotics were determined, among which aminoglycosides, β-lactams, ansamycins, peptides, macrolides were majority. The relative abundances of detected ABGs had a large interval, ranging from 0.000006% to 0.042%. The predominant antibiotic types of synthetic genes with higher relative expression levels were monobactams, penicillin & cephalosporins and streptomycin, primarily belonging to β-lactams and aminoglycosides. The hypothetical synthetic pathways of streptomycin synthesis and penicillin & cephalosporin synthesis were proposed. And the coexistence of ABGs and ARGs for these two antibiotics was also pronounced in activated sludge from meta-omics data. These findings for the first time demonstrated the antibiotic synthetic potential in activated sludges, revealing new sources of antibiotics and resistance genes in WWTPs, and thereby aggravating environmental pollution.
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Affiliation(s)
- Yu Huang
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China
| | - Kui Zou
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China
| | - Taiping Qing
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China
| | - Bo Feng
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China
| | - Peng Zhang
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China.
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6
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Fierro F, Vaca I, Castillo NI, García-Rico RO, Chávez R. Penicillium chrysogenum, a Vintage Model with a Cutting-Edge Profile in Biotechnology. Microorganisms 2022; 10:microorganisms10030573. [PMID: 35336148 PMCID: PMC8954384 DOI: 10.3390/microorganisms10030573] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 12/20/2022] Open
Abstract
The discovery of penicillin entailed a decisive breakthrough in medicine. No other medical advance has ever had the same impact in the clinical practise. The fungus Penicillium chrysogenum (reclassified as P. rubens) has been used for industrial production of penicillin ever since the forties of the past century; industrial biotechnology developed hand in hand with it, and currently P. chrysogenum is a thoroughly studied model for secondary metabolite production and regulation. In addition to its role as penicillin producer, recent synthetic biology advances have put P. chrysogenum on the path to become a cell factory for the production of metabolites with biotechnological interest. In this review, we tell the history of P. chrysogenum, from the discovery of penicillin and the first isolation of strains with high production capacity to the most recent research advances with the fungus. We will describe how classical strain improvement programs achieved the goal of increasing production and how the development of different molecular tools allowed further improvements. The discovery of the penicillin gene cluster, the origin of the penicillin genes, the regulation of penicillin production, and a compilation of other P. chrysogenum secondary metabolites will also be covered and updated in this work.
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Affiliation(s)
- Francisco Fierro
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Unidad Iztapalapa, Ciudad de México 09340, Mexico
- Correspondence:
| | - Inmaculada Vaca
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile;
| | - Nancy I. Castillo
- Grupo de Investigación en Ciencias Biológicas y Químicas, Facultad de Ciencias, Universidad Antonio Nariño, Bogotá 110231, Colombia;
| | - Ramón Ovidio García-Rico
- Grupo de Investigación GIMBIO, Departamento De Microbiología, Facultad de Ciencias Básicas, Universidad de Pamplona, Pamplona 543050, Colombia;
| | - Renato Chávez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago 9170020, Chile;
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Iacovelli R, Mózsik L, Bovenberg RA, Driessen AJ. Identification of a conserved N-terminal domain in the first module of ACV synthetases. Microbiologyopen 2021; 10:e1145. [PMID: 33449449 PMCID: PMC7884236 DOI: 10.1002/mbo3.1145] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/25/2020] [Accepted: 11/28/2020] [Indexed: 11/25/2022] Open
Abstract
The l-δ-(α-aminoadipoyl)-l-cysteinyl-d-valine synthetase (ACVS) is a trimodular nonribosomal peptide synthetase (NRPS) that provides the peptide precursor for the synthesis of β-lactams. The enzyme has been extensively characterized in terms of tripeptide formation and substrate specificity. The first module is highly specific and is the only NRPS unit known to recruit and activate the substrate l-α-aminoadipic acid, which is coupled to the α-amino group of l-cysteine through an unusual peptide bond, involving its δ-carboxyl group. Here we carried out an in-depth investigation on the architecture of the first module of the ACVS enzymes from the fungus Penicillium rubens and the bacterium Nocardia lactamdurans. Bioinformatic analyses revealed the presence of a previously unidentified domain at the N-terminus which is structurally related to condensation domains, but smaller in size. Deletion variants of both enzymes were generated to investigate the potential impact on penicillin biosynthesis in vivo and in vitro. The data indicate that the N-terminal domain is important for catalysis.
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Affiliation(s)
- Riccardo Iacovelli
- Molecular MicrobiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - László Mózsik
- Molecular MicrobiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Roel A.L. Bovenberg
- Synthetic Biology and Cell EngineeringGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
- DSM Biotechnology CentreDelftThe Netherlands
| | - Arnold J.M. Driessen
- Molecular MicrobiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
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8
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Kozuch J, Schneider SH, Boxer SG. Biosynthetic Incorporation of Site-Specific Isotopes in β-Lactam Antibiotics Enables Biophysical Studies. ACS Chem Biol 2020; 15:1148-1153. [PMID: 32175720 DOI: 10.1021/acschembio.9b01054] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A biophysical understanding of the mechanistic, chemical, and physical origins underlying antibiotic action and resistance is vital to the discovery of novel therapeutics and the development of strategies to combat the growing emergence of antibiotic resistance. The site-specific introduction of stable-isotope labels into chemically complex natural products is particularly important for techniques such as NMR, IR, mass spectrometry, imaging, and kinetic isotope effects. Toward this goal, we developed a biosynthetic strategy for the site-specific incorporation of 13C labels into the canonical β-lactam carbonyl of penicillin G and cefotaxime, the latter via cephalosporin C. This was achieved through sulfur-replacement with 1-13C-l-cysteine, resulting in high isotope incorporations and milligram-scale yields. Using 13C NMR and isotope-edited IR difference spectroscopy, we illustrate how these molecules can be used to interrogate interactions with their protein targets, e.g., TEM-1 β-lactamase. This method provides a feasible route to isotopically labeled penicillin and cephalosporin precursors for future biophysical studies.
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Affiliation(s)
- Jacek Kozuch
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
| | - Samuel H. Schneider
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
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9
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Mózsik L, Büttel Z, Bovenberg RAL, Driessen AJM, Nygård Y. Synthetic control devices for gene regulation in Penicillium chrysogenum. Microb Cell Fact 2019; 18:203. [PMID: 31739777 PMCID: PMC6859608 DOI: 10.1186/s12934-019-1253-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 11/10/2019] [Indexed: 12/01/2022] Open
Abstract
Background Orthogonal, synthetic control devices were developed for Penicillium chrysogenum, a model filamentous fungus and industrially relevant cell factory. In the synthetic transcription factor, the QF DNA-binding domain of the transcription factor of the quinic acid gene cluster of Neurospora crassa is fused to the VP16 activation domain. This synthetic transcription factor controls the expression of genes under a synthetic promoter containing quinic acid upstream activating sequence (QUAS) elements, where it binds. A gene cluster may demand an expression tuned individually for each gene, which is a great advantage provided by this system. Results The control devices were characterized with respect to three of their main components: expression of the synthetic transcription factors, upstream activating sequences, and the affinity of the DNA binding domain of the transcription factor to the upstream activating domain. This resulted in synthetic expression devices, with an expression ranging from hardly detectable to a level similar to that of highest expressed native genes. The versatility of the control device was demonstrated by fluorescent reporters and its application was confirmed by synthetically controlling the production of penicillin. Conclusions The characterization of the control devices in microbioreactors, proved to give excellent indications for how the devices function in production strains and conditions. We anticipate that these well-characterized and robustly performing control devices can be widely applied for the production of secondary metabolites and other compounds in filamentous fungi.![]()
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Affiliation(s)
- László Mózsik
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Zsófia Büttel
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Roel A L Bovenberg
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands.,Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Arnold J M Driessen
- 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. .,DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands. .,Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden.
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10
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Zhgun AA, Nuraeva GK, Dumina MV, Voinova TM, Dzhavakhiya VV, Eldarov MA. 1,3-Diaminopropane and Spermidine Upregulate Lovastatin Production and Expression of Lovastatin Biosynthetic Genes in Aspergillus terreus via LaeA Regulation. APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683819020170] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Telke AA, Ovchinnikov KV, Vuoristo KS, Mathiesen G, Thorstensen T, Diep DB. Over 2000-Fold Increased Production of the Leaderless Bacteriocin Garvicin KS by Increasing Gene Dose and Optimization of Culture Conditions. Front Microbiol 2019; 10:389. [PMID: 30891018 PMCID: PMC6412029 DOI: 10.3389/fmicb.2019.00389] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 02/13/2019] [Indexed: 11/21/2022] Open
Abstract
The leaderless bacteriocin Garvicin KS (GarKS) is a potent antimicrobial, being active against a wide range of important pathogens. GarKS production by the native producer Lactococcus garvieae KS1546 is, however, relatively low (80 BU/ml) under standard laboratory growth conditions (batch culture in GM17 at 30°C). To improve the production, we systematically evaluated the impact of different media and media components on bacteriocin production. Based on the outcomes, a new medium formulation was made that increased GarKS production about 60-fold compared to that achieved in GM17. The new medium was composed of pasteurized milk and tryptone (PM-T). GarKS production was increased further 4-fold (i.e., to 20,000 BU/ml) by increasing the gene dose of the bacteriocin gene cluster (gak) in the native producer. Finally, a combination of the newly composed medium (PM-T), an increased gene dose and cultivation at a constant pH 6 and a 50-60% dissolved oxygen level in growth medium, gave rise to a GarKS production of 164,000 BU/ml. This high production, which is about 2000-fold higher compared to that initially achieved in GM17, corresponds to a GarKS production of 1.2 g/L. To our knowledge, this is one of the highest bacteriocin production reported hitherto.
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Affiliation(s)
| | | | | | | | | | - Dzung B. Diep
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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12
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Guzmán-Chávez F, Zwahlen RD, Bovenberg RAL, Driessen AJM. Engineering of the Filamentous Fungus Penicillium chrysogenum as Cell Factory for Natural Products. Front Microbiol 2018; 9:2768. [PMID: 30524395 PMCID: PMC6262359 DOI: 10.3389/fmicb.2018.02768] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/29/2018] [Indexed: 12/14/2022] Open
Abstract
Penicillium chrysogenum (renamed P. rubens) is the most studied member of a family of more than 350 Penicillium species that constitute the genus. Since the discovery of penicillin by Alexander Fleming, this filamentous fungus is used as a commercial β-lactam antibiotic producer. For several decades, P. chrysogenum was subjected to a classical strain improvement (CSI) program to increase penicillin titers. This resulted in a massive increase in the penicillin production capacity, paralleled by the silencing of several other biosynthetic gene clusters (BGCs), causing a reduction in the production of a broad range of BGC encoded natural products (NPs). Several approaches have been used to restore the ability of the penicillin production strains to synthetize the NPs lost during the CSI. Here, we summarize various re-activation mechanisms of BGCs, and how interference with regulation can be used as a strategy to activate or silence BGCs in filamentous fungi. To further emphasize the versatility of P. chrysogenum as a fungal production platform for NPs with potential commercial value, protein engineering of biosynthetic enzymes is discussed as a tool to develop de novo BGC pathways for new NPs.
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Affiliation(s)
- Fernando Guzmán-Chávez
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Reto D Zwahlen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Roel A L Bovenberg
- Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,DSM Biotechnology Centre, Delft, Netherlands
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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13
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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] [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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Massonnet M, Morales-Cruz A, Minio A, Figueroa-Balderas R, Lawrence DP, Travadon R, Rolshausen PE, Baumgartner K, Cantu D. Whole-Genome Resequencing and Pan-Transcriptome Reconstruction Highlight the Impact of Genomic Structural Variation on Secondary Metabolite Gene Clusters in the Grapevine Esca Pathogen Phaeoacremonium minimum. Front Microbiol 2018; 9:1784. [PMID: 30150972 PMCID: PMC6099105 DOI: 10.3389/fmicb.2018.01784] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 07/16/2018] [Indexed: 12/30/2022] Open
Abstract
The Ascomycete fungus Phaeoacremonium minimum is one of the primary causal agents of Esca, a widespread and damaging grapevine trunk disease. Variation in virulence among Pm. minimum isolates has been reported, but the underlying genetic basis of the phenotypic variability remains unknown. The goal of this study was to characterize intraspecific genetic diversity and explore its potential impact on virulence functions associated with secondary metabolism, cellular transport, and cell wall decomposition. We generated a chromosome-scale genome assembly, using single molecule real-time sequencing, and resequenced the genomes and transcriptomes of multiple isolates to identify sequence and structural polymorphisms. Numerous insertion and deletion events were found for a total of about 1 Mbp in each isolate. Structural variation in this extremely gene dense genome frequently caused presence/absence polymorphisms of multiple adjacent genes, mostly belonging to biosynthetic clusters associated with secondary metabolism. Because of the observed intraspecific diversity in gene content due to structural variation we concluded that a transcriptome reference developed from a single isolate is insufficient to represent the virulence factor repertoire of the species. We therefore compiled a pan-transcriptome reference of Pm. minimum comprising a non-redundant set of 15,245 protein-coding sequences. Using naturally infected field samples expressing Esca symptoms, we demonstrated that mapping of meta-transcriptomics data on a multi-species reference that included the Pm. minimum pan-transcriptome allows the profiling of an expanded set of virulence factors, including variable genes associated with secondary metabolism and cellular transport.
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Affiliation(s)
- Mélanie Massonnet
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - Abraham Morales-Cruz
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - Andrea Minio
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - Daniel P. Lawrence
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Renaud Travadon
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Philippe E. Rolshausen
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Kendra Baumgartner
- Crops Pathology and Genetics Research Unit, Agricultural Research Service, United States Department of Agriculture, Davis, CA, United States
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
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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: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [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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Ziemons S, Koutsantas K, Becker K, Dahlmann T, Kück U. Penicillin production in industrial strain Penicillium chrysogenum P2niaD18 is not dependent on the copy number of biosynthesis genes. BMC Biotechnol 2017; 17:16. [PMID: 28209150 PMCID: PMC5314624 DOI: 10.1186/s12896-017-0335-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 02/09/2017] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Multi-copy gene integration into microbial genomes is a conventional tool for obtaining improved gene expression. For Penicillium chrysogenum, the fungal producer of the beta-lactam antibiotic penicillin, many production strains carry multiple copies of the penicillin biosynthesis gene cluster. This discovery led to the generally accepted view that high penicillin titers are the result of multiple copies of penicillin genes. Here we investigated strain P2niaD18, a production line that carries only two copies of the penicillin gene cluster. RESULTS We performed pulsed-field gel electrophoresis (PFGE), quantitative qRT-PCR, and penicillin bioassays to investigate production, deletion and overexpression strains generated in the P. chrysogenum P2niaD18 background, in order to determine the copy number of the penicillin biosynthesis gene cluster, and study the expression of one penicillin biosynthesis gene, and the penicillin titer. Analysis of production and recombinant strain showed that the enhanced penicillin titer did not depend on the copy number of the penicillin gene cluster. Our assumption was strengthened by results with a penicillin null strain lacking pcbC encoding isopenicillin N synthase. Reintroduction of one or two copies of the cluster into the pcbC deletion strain restored transcriptional high expression of the pcbC gene, but recombinant strains showed no significantly different penicillin titer compared to parental strains. CONCLUSIONS Here we present a molecular genetic analysis of production and recombinant strains in the P2niaD18 background carrying different copy numbers of the penicillin biosynthesis gene cluster. Our analysis shows that the enhanced penicillin titer does not strictly depend on the copy number of the cluster. Based on these overall findings, we hypothesize that instead, complex regulatory mechanisms are prominently implicated in increased penicillin biosynthesis in production strains.
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Affiliation(s)
- Sandra Ziemons
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, ND7/131, Universitätsstraße 150, 44780, Bochum, Germany
| | - Katerina Koutsantas
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, ND7/131, Universitätsstraße 150, 44780, Bochum, Germany
| | - Kordula Becker
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, ND7/131, Universitätsstraße 150, 44780, Bochum, Germany
| | - Tim Dahlmann
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, ND7/131, Universitätsstraße 150, 44780, Bochum, Germany
| | - Ulrich Kück
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, ND7/131, Universitätsstraße 150, 44780, Bochum, Germany.
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Polli F, Meijrink B, Bovenberg RA, Driessen AJ. New promoters for strain engineering of Penicillium chrysogenum. Fungal Genet Biol 2016; 89:62-71. [DOI: 10.1016/j.fgb.2015.12.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 11/23/2015] [Accepted: 12/05/2015] [Indexed: 10/22/2022]
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Salo OV, Ries M, Medema MH, Lankhorst PP, Vreeken RJ, Bovenberg RAL, Driessen AJM. Genomic mutational analysis of the impact of the classical strain improvement program on β-lactam producing Penicillium chrysogenum. BMC Genomics 2015; 16:937. [PMID: 26572918 PMCID: PMC4647614 DOI: 10.1186/s12864-015-2154-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/27/2015] [Indexed: 12/04/2022] Open
Abstract
Background Penicillium chrysogenum is a filamentous fungus that is employed as an industrial producer of β–lactams. The high β–lactam titers of current strains is the result of a classical strain improvement program (CSI) starting with a wild-type like strain more than six decades ago. This involved extensive mutagenesis and strain selection for improved β–lactam titers and growth characteristics. However, the impact of the CSI on the secondary metabolism in general remains unknown. Results To examine the impact of CSI on secondary metabolism, a comparative genomic analysis of β-lactam producing strains was carried out by genome sequencing of three P. chrysogenum strains that are part of a lineage of the CSI, i.e., strains NRRL1951, Wisconsin 54-1255, DS17690, and the derived penicillin biosynthesis cluster free strain DS68530. CSI has resulted in a wide spread of mutations, that statistically did not result in an over- or underrepresentation of specific gene classes. However, in this set of mutations, 8 out of 31 secondary metabolite genes (20 polyketide synthases and 11 non-ribosomal peptide synthetases) were targeted with a corresponding and progressive loss in the production of a range of secondary metabolites unrelated to β–lactam production. Additionally, key Velvet complex proteins (LeaA and VelA) involved in global regulation of secondary metabolism have been repeatedly targeted for mutagenesis during CSI. Using comparative metabolic profiling, the polyketide synthetase gene cluster was identified that is responsible for sorbicillinoid biosynthesis, a group of yellow-colored metabolites that are abundantly produced by early production strains of P. chrysogenum. Conclusions The classical industrial strain improvement of P. chrysogenum has had a broad mutagenic impact on metabolism and has resulted in silencing of specific secondary metabolite genes with the concomitant diversion of metabolism towards the production of β–lactams. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2154-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Oleksandr V Salo
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
| | - Marco Ries
- Division of Analytical Biosciences, Leiden/Amsterdam Center for Drug Research, Leiden, The Netherlands. .,Netherlands Metabolomics Centre, Leiden University, Leiden, The Netherlands.
| | - Marnix H Medema
- Bioinformatics, Wageningen University, Wageningen, The Netherlands.
| | | | - Rob J Vreeken
- Division of Analytical Biosciences, Leiden/Amsterdam Center for Drug Research, Leiden, The Netherlands. .,Netherlands Metabolomics Centre, Leiden University, Leiden, The Netherlands.
| | - Roel A L Bovenberg
- DSM Biotechnology Centre, Delft, The Netherlands. .,Synthetic Biology and Cell Engineering, 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. .,Kluyver Centre for Genomics of Industrial Fermentations, Julianalaan 67, 2628BC, Delft, The Netherlands.
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19
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In vivo kinetic analysis of the penicillin biosynthesis pathway using PAA stimulus response experiments. Metab Eng 2015; 32:155-173. [DOI: 10.1016/j.ymben.2015.09.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 09/22/2015] [Accepted: 09/26/2015] [Indexed: 11/18/2022]
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Abstract
Natural products are important sources of pharmaceuticals, in part owing to their diverse biological activities. Enzymes from natural product biosynthetic pathways have become attractive candidates as biocatalysts for modifying the structures and bioactivities of these complex compounds. Numerous enzymes have been harvested to generate innovative scaffolds, large-scale synthesis of chiral building blocks, and semisynthesis of medicinally relevant natural product derivatives. This review discusses recent examples from three areas: (a) polyketide catalytic domain engineering geared toward synthesis of new polyketides, (b) engineering of tailoring enzymes (other than oxidative enzymes) as biocatalysts, and (c) in vitro total synthesis of natural products using purified enzyme components. With the availability of exponentially increasing genomic information and new genome mining tools, many new and powerful biocatalysts tailored for pharmaceutical synthesis will likely emerge from secondary metabolism.
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Sharma M, Sharma R. Drugs and drug intermediates from fungi: Striving for greener processes. Crit Rev Microbiol 2014; 42:322-38. [PMID: 25159041 DOI: 10.3109/1040841x.2014.947240] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
There is an ever-increasing demand of newer and improved drugs from biological sources to cater to the bio-pharmaceutical sector. Among various other resources, fungal species have an immense contribution owing to their potential to carry out the bio-transformations and drug synthesis in diverse conditions and in an eco-friendly manner. Advancement in the biotechnological processes has accelerated the process. Genome sequence information of various fungal species has opened newer avenues for improved and faster drug targeting and designing. The review highlights the production of pharmaceutical drugs and drug intermediates like antibiotics, anti-cancer, anti-cholesterol, anti-diabetic, immunosuppressant, anti-anxiety, anti-virals and many other drugs from fungus. Many of these have been commercialized and there are many more which are either in research or in clinical trial phase. There is a need to exploit and explore the vast biota of fungi in the hope of discovering untapped therapeutic uses of the earth's countless species of fungus.
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Affiliation(s)
- Monika Sharma
- a Department of Biotechnology , Panjab University , Chandigarh , India and
| | - Rohit Sharma
- b Centre for Microbial Biotechnology, Panjab University , Chandigarh , India
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23
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Scheckhuber CQ, Veenhuis M, van der Klei IJ. Improving penicillin biosynthesis in Penicillium chrysogenum by glyoxalase overproduction. Metab Eng 2013; 18:36-43. [DOI: 10.1016/j.ymben.2013.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 04/02/2013] [Accepted: 04/03/2013] [Indexed: 11/25/2022]
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Exploring antibiotic biosynthesis: Leo Vining's insights lead to new strategies in the quest for 'The 10 × '20 Initiative'. J Antibiot (Tokyo) 2013; 66:365-9. [PMID: 23695415 DOI: 10.1038/ja.2013.46] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2013] [Revised: 04/02/2013] [Accepted: 04/12/2013] [Indexed: 11/08/2022]
Abstract
The late Professor Leo Vining began his antibiotics research career as a visiting scientist in the laboratory of Selman Waksman at Rutgers University during the golden age of antibiotics. Through six decades of his distinguished career, Vining explored the biosynthesis of dozens of antibacterial and antifungal compounds produced by microorganisms. A number of underlying mechanisms of antibiotic biosynthesis were unraveled through his holistic approach and the findings laid the foundation to our understanding of regulation of antibiotic biosynthesis. In this paper, we reflect on Professor Vining's antibiotic research philosophy from a personal perspective and connect this philosophy to new approaches for rapid development of the next generation of antibiotics, which is urgently needed to combat the threat of escalating antimicrobial resistance. Facing the urgency, The Infectious Disease Society of America launched 'The 10 × '20 Initiative' in 2010 and called for a global commitment to develop 10 new, safe and effective antibiotics by the year 2020.(1.)
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25
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Recent advances in the biosynthesis of penicillins, cephalosporins and clavams and its regulation. Biotechnol Adv 2013; 31:287-311. [DOI: 10.1016/j.biotechadv.2012.12.001] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 11/30/2012] [Accepted: 12/01/2012] [Indexed: 11/23/2022]
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26
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The ABC transporter ABC40 encodes a phenylacetic acid export system in Penicillium chrysogenum. Fungal Genet Biol 2012; 49:915-21. [DOI: 10.1016/j.fgb.2012.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 09/08/2012] [Accepted: 09/10/2012] [Indexed: 11/23/2022]
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Increased penicillin production in Penicillium chrysogenum production strains via balanced overexpression of isopenicillin N acyltransferase. Appl Environ Microbiol 2012; 78:7107-13. [PMID: 22865068 DOI: 10.1128/aem.01529-12] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Intense classical strain improvement has yielded industrial Penicillium chrysogenum strains that produce high titers of penicillin. These strains contain multiple copies of the penicillin biosynthesis cluster encoding the three key enzymes: δ-(l-α-aminoadipyl)-L-cysteinyl-D-valine synthetase (ACVS), isopenicillin N synthase (IPNS), and isopenicillin N acyltransferase (IAT). The phenylacetic acid coenzyme A (CoA) ligase (PCL) gene encoding the enzyme responsible for the activation of the side chain precursor phenylacetic acid is localized elsewhere in the genome in a single copy. Since the protein level of IAT already saturates at low cluster copy numbers, IAT might catalyze a limiting step in high-yielding strains. Here, we show that penicillin production in high-yielding strains can be further improved by the overexpression of IAT while at very high levels of IAT the precursor 6-aminopenicillic acid (6-APA) accumulates. Overproduction of PCL only marginally stimulates penicillin production. These data demonstrate that in high-yielding strains IAT is the limiting factor and that this limitation can be alleviated by a balanced overproduction of this enzyme.
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Veiga T, Gombert AK, Landes N, Verhoeven MD, Kiel JA, Krikken AM, Nijland JG, Touw H, Luttik MA, van der Toorn JC, Driessen AJ, Bovenberg RA, van den Berg MA, van der Klei IJ, Pronk JT, Daran JM. Metabolic engineering of β-oxidation in Penicillium chrysogenum for improved semi-synthetic cephalosporin biosynthesis. Metab Eng 2012; 14:437-48. [DOI: 10.1016/j.ymben.2012.02.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 01/13/2012] [Accepted: 02/13/2012] [Indexed: 11/25/2022]
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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 : A JOURNAL OF INTEGRATIVE BIOLOGY 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] [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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30
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Proteomics shows new faces for the old penicillin producer Penicillium chrysogenum. J Biomed Biotechnol 2012; 2012:105109. [PMID: 22318718 PMCID: PMC3270403 DOI: 10.1155/2012/105109] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 09/30/2011] [Accepted: 10/14/2011] [Indexed: 12/14/2022] Open
Abstract
Fungi comprise a vast group of microorganisms including the Ascomycota (majority of all described fungi), the Basidiomycota (mushrooms or higher fungi), and the Zygomycota and Chytridiomycota (basal or lower fungi) that produce industrially interesting secondary metabolites, such as β-lactam antibiotics. These compounds are one of the most commonly prescribed drugs world-wide. Since Fleming's initial discovery of Penicillium notatum 80 years ago, the role of Penicillium as an antimicrobial source became patent. After the isolation of Penicillium chrysogenum NRRL 1951 six decades ago, classical mutagenesis and screening programs led to the development of industrial strains with increased productivity (at least three orders of magnitude). The new “omics” era has provided the key to understand the underlying mechanisms of the industrial strain improvement process. The review of different proteomics methods applied to P. chrysogenum has revealed that industrial modification of this microorganism was a consequence of a careful rebalancing of several metabolic pathways. In addition, the secretome analysis of P. chrysogenum has opened the door to new industrial applications for this versatile filamentous fungus.
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31
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de Jonge LP, Buijs NAA, ten Pierick A, Deshmukh A, Zhao Z, Kiel JAKW, Heijnen JJ, van Gulik WM. Scale-down of penicillin production in Penicillium chrysogenum. Biotechnol J 2011; 6:944-58. [PMID: 21751388 DOI: 10.1002/biot.201000409] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In large-scale production reactors the combination of high broth viscosity and large broth volume leads to insufficient liquid-phase mixing, resulting in gradients in, for example, the concentrations of substrate and oxygen. This often leads to differences in productivity of the full-scale process compared with laboratory scale. In this scale-down study of penicillin production, the influence of substrate gradients on process performance and cell physiology was investigated by imposing an intermittent feeding regime on a laboratory-scale culture of a high yielding strain of Penicillium chrysogenum. It was found that penicillin production was reduced by a factor of two in the intermittently fed cultures relative to constant feed cultivations fed with the same amount of glucose per hour, while the biomass yield was the same. Measurement of the levels of the intermediates of the penicillin biosynthesis pathway, along with the enzyme levels, suggested that the reduction of the flux through the penicillin pathway is mainly the result of a lower influx into the pathway, possibly due to inhibitory levels of adenosine monophosphate and pyrophosphate and lower activating levels of adenosine triphosphate during the zero-substrate phase of each cycle of intermittent feeding.
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Affiliation(s)
- Lodewijk P de Jonge
- Bioprocess Technology, Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
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32
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Weber SS, Bovenberg RAL, Driessen AJM. Biosynthetic concepts for the production of β-lactam antibiotics in Penicillium chrysogenum. Biotechnol J 2011; 7:225-36. [PMID: 22057844 DOI: 10.1002/biot.201100065] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2011] [Revised: 08/12/2011] [Accepted: 08/24/2011] [Indexed: 11/08/2022]
Abstract
Industrial production of β-lactam antibiotics by the filamentous fungus Penicillium chrysogenum is based on successive classical strain improvement cycles. This review summarizes our current knowledge on the results of this classical strain improvement process, and discusses avenues to improve β-lactam biosynthesis and to exploit P. chrysogenum as an industrial host for the production of other antibiotics and peptide products. Genomic and transcriptional analysis of strain lineages has led to the identification of several important alterations in high-yielding strains, including the amplification of the penicillin biosynthetic gene cluster, elevated transcription of genes involved in biosynthesis of penicillin and amino acid precursors, and genes encoding microbody proliferation factors. In recent years, successful metabolic engineering and synthetic biology approaches have resulted in the redirection of the penicillin pathway towards the production of cephalosporins. This sets a new direction in industrial antibiotics productions towards more sustainable methods for the fermentative production of unnatural antibiotics and related compounds.
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Affiliation(s)
- Stefan S Weber
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Zernike Institute for Advanced Materials and Kluyver Center for Genomics of Industrial Fermentation, AG Groningen, The Netherlands
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Impact of the Penicillium chrysogenum genome on industrial production of metabolites. Appl Microbiol Biotechnol 2011; 92:45-53. [PMID: 21805169 DOI: 10.1007/s00253-011-3476-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2011] [Revised: 06/27/2011] [Accepted: 07/13/2011] [Indexed: 01/12/2023]
Abstract
The genome sequence of Penicillium chrysogenum has initiated a range of fundamental studies, deciphering the genetic secrets of the industrial penicillin producer. More than 60 years of classical strain improvement has resulted in major but delicate rebalancing of the intracellular metabolism leading to the impressive penicillin titres of the current production strains. Several leads for further improvement are being followed up, including the use of P. chrysogenum as a cell factory for other products than β-lactam antibiotics.
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