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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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2
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Zhao J, Muawiya MA, Zhuang Y, Wang G. Developing rational scale-down simulators for mimicking substrate heterogeneities based on cell lifelines in industrial-scale bioreactors. BIORESOURCE TECHNOLOGY 2024; 395:130354. [PMID: 38272147 DOI: 10.1016/j.biortech.2024.130354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024]
Abstract
The influence of extracellular variations on the cellular metabolism and thereby the process performance at large-scale can be evaluated using the so-called scale-down simulators. Nevertheless, the major challenge is to design an appropriate scale-down simulator, which can accurately mimic the cell lifelines that record the flow paths and experiences of cells circulating in large-scale bioreactors. To address this, a dedicated SDSA (scale-down simulator application) was purposedly developed on the basis of black box model and process reaction model established for Penicillium chrysogenum strain as well as cell lifelines or trajectories information in an industrial-scale fermentor. Guided by the SDSA, the industrial-relevant metabolic regimes for substrate availability, i.e., excess, limitation and starvation, were successfully reproduced at laboratory-scale three-compartment scale-down (SD) system. In addition, such SDSA can also display individual process dynamics in each compartment, and demonstrate how individual factors influence the entire bioprocess performance, thus serving both educational and research purposes.
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Affiliation(s)
- Jiachen Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China
| | - Muhammad Alkali Muawiya
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China
| | - Guan Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, People's Republic of China.
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Janoska A, Verheijen JJ, Tang W, Lee Q, Sikkema B, van Gulik WM. Influence of oxygen concentration on the metabolism of Penicillium chrysogenum. Eng Life Sci 2022; 23:e2100139. [PMID: 36619886 PMCID: PMC9815084 DOI: 10.1002/elsc.202100139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/17/2022] [Accepted: 03/08/2022] [Indexed: 01/11/2023] Open
Abstract
In large-scale bioreactors, there is often insufficient mixing and as a consequence, cells experience uneven substrate and oxygen levels that influence product formation. In this study, the influence of dissolved oxygen (DO) gradients on the primary and secondary metabolism of a high producing industrial strain of Penicillium chrysogenum was investigated. Within a wide range of DO concentrations, obtained under chemostat conditions, we observed different responses from P. chrysogenum: (i) no influence on growth or penicillin production (>0.025 mmol L-1); (ii) reduced penicillin production, but no growth limitation (0.013-0.025 mmol L-1); and (iii) growth and penicillin production limitations (<0.013 mmol L-1). In addition, scale down experiments were performed by oscillating the DO concentration in the bioreactor. We found that during DO oscillation, the penicillin production rate decreased below the value observed when a constant DO equal to the average oscillating DO value was used. To understand and predict the influence of oxygen levels on primary metabolism and penicillin production, we developed a black box model that was linked to a detailed kinetic model of the penicillin pathway. The model simulations represented the experimental data during the step experiments; however, during the oscillation experiments the predictions deviated, indicating the involvement of the central metabolism in penicillin production.
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Affiliation(s)
- Agnes Janoska
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Jelle J. Verheijen
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Wenjung Tang
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands,DSM Biotechnology CenterAlexander Fleminglaan 1DelftNetherlands
| | - Queenie Lee
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Baukje Sikkema
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Walter M. van Gulik
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
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Song H, Bao Y, Zhang M, Liu S, Yu C, Dai J, Wu C, Tang D, Fang W. An inactivating mutation in the vacuolar arginine exporter gene Vae results in culture degeneration in the fungus Metarhizium robertsii. Environ Microbiol 2022; 24:2924-2937. [PMID: 35352870 DOI: 10.1111/1462-2920.15982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 03/03/2022] [Accepted: 03/20/2022] [Indexed: 02/04/2023]
Abstract
Culture degeneration usually results in great commercial losses in the economically important filamentous fungi, but the genetic causes of the degeneration remain elusive. In the fungus Metarhizium robertsii, we found that deletion of the vacuolar arginine exporter gene Vae caused culture degeneration. Compared to the WT strain, the mutant showed increased apoptosis, reactive oxygen species (ROS) level and mitochondrial membrane potential collapse, reduced conidial yield and abnormal lipid droplet formation. The extent of the degeneration in the mutant gradually increased over the successive subculturing, which eventually became irreversible; compared to the third subculture of the mutant, the seventh subculture showed a lower conidial yield and pathogenicity to insects, stronger apoptosis, higher ROS level and a smaller number of conidial lipid droplets. Incorporation of the genomic clone of Vae could not restore the WT phenotypes in the seventh subculture, but could in the third one. Loss-of-function in Vae resulted in vacuolar arginine accumulation and reduction in the cytosolic arginine. This downregulated the expression of the regulator CAG9 of G protein signalling pathway, which accounted for most of the phenotypic changes associated with the degeneration of the mutant. We identified a deleterious mutation that causes culture degeneration in a filamentous fugus.
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Affiliation(s)
- Hui Song
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Science, Zhejiang University, Hangzhou, China
| | - Yuting Bao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Science, Zhejiang University, Hangzhou, China
| | - Mingxiang Zhang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Science, Zhejiang University, Hangzhou, China
| | - Shuxing Liu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Science, Zhejiang University, Hangzhou, China
| | - Chaonan Yu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Science, Zhejiang University, Hangzhou, China
| | - Jin Dai
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Science, Zhejiang University, Hangzhou, China
| | - Congcong Wu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Science, Zhejiang University, Hangzhou, China
| | - Dan Tang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Science, Zhejiang University, Hangzhou, China
| | - Weiguo Fang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Science, Zhejiang University, Hangzhou, China
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Impact of Altered Trehalose Metabolism on Physiological Response of Penicillium chrysogenum Chemostat Cultures during Industrially Relevant Rapid Feast/Famine Conditions. Processes (Basel) 2021. [DOI: 10.3390/pr9010118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Due to insufficient mass transfer and mixing issues, cells in the industrial-scale bioreactor are often forced to experience glucose feast/famine cycles, mostly resulting in reduced commercial metrics (titer, yield and productivity). Trehalose cycling has been confirmed as a double-edged sword in the Penicillium chrysogenum strain, which facilitates the maintenance of a metabolically balanced state, but it consumes extra amounts of the ATP responsible for the repeated breakdown and formation of trehalose molecules in response to extracellular glucose perturbations. This loss of ATP would be in competition with the high ATP-demanding penicillin biosynthesis. In this work, the role of trehalose metabolism was further explored under industrially relevant conditions by cultivating a high-yielding Penicillium chrysogenum strain, and the derived trehalose-null strains in the glucose-limited chemostat system where the glucose feast/famine condition was imposed. This dynamic feast/famine regime with a block-wise feed/no feed regime (36 s on, 324 s off) allows one to generate repetitive cycles of moderate changes in glucose availability. The results obtained using quantitative metabolomics and stoichiometric analysis revealed that the intact trehalose metabolism is vitally important for maintaining penicillin production capacity in the Penicillium chrysogenum strain under both steady state and dynamic conditions. Additionally, cells lacking such a key metabolic regulator would become more sensitive to industrially relevant conditions, and are more able to sustain metabolic rearrangements, which manifests in the shrinkage of the central metabolite pool size and the formation of ATP-consuming futile cycles.
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Wright NR, Rønnest NP, Sonnenschein N. Single-Cell Technologies to Understand the Mechanisms of Cellular Adaptation in Chemostats. Front Bioeng Biotechnol 2020; 8:579841. [PMID: 33392163 PMCID: PMC7775484 DOI: 10.3389/fbioe.2020.579841] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022] Open
Abstract
There is a growing interest in continuous manufacturing within the bioprocessing community. In this context, the chemostat process is an important unit operation. The current application of chemostat processes in industry is limited although many high yielding processes are reported in literature. In order to reach the full potential of the chemostat in continuous manufacture, the output should be constant. However, adaptation is often observed resulting in changed productivities over time. The observed adaptation can be coupled to the selective pressure of the nutrient-limited environment in the chemostat. We argue that population heterogeneity should be taken into account when studying adaptation in the chemostat. We propose to investigate adaptation at the single-cell level and discuss the potential of different single-cell technologies, which could be used to increase the understanding of the phenomena. Currently, none of the discussed single-cell technologies fulfill all our criteria but in combination they may reveal important information, which can be used to understand and potentially control the adaptation.
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Affiliation(s)
- Naia Risager Wright
- Novo Nordisk A/S, Bagsvaerd, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Nikolaus Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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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] [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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Anticancer activity and metabolite profiling data of Penicillium janthinellum KTMT5. Data Brief 2020; 28:104959. [PMID: 31890800 PMCID: PMC6928313 DOI: 10.1016/j.dib.2019.104959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 11/22/2022] Open
Abstract
Fungi are ubiquitous, they proliferate even in environments with toxic pollutants that are otherwise harmful to other eukaryotes. This article presents data of fungi which were isolated from gold mine tailings and identified by DNA sequencing of their inter transcribed spacer regions 1 and 2. Five fungal isolates were identified, among which the crude extract of Penicillium janthinellum KTMT5 was investigated for anticancer activity on A549 (lung carcinoma) and UMG87 (glioblastoma) cell lines. Untargeted metabolite profiling of the crude extract of P. janthinellum KTMT5 was performed using liquid chromatography quadrupole time of flight tandem mass spectrometry (LC-QTOF-MS/MS) and a molecular network generated using the online workflow on the Global Natural Product Social molecular networking (GNPS) website. DNA sequencing showed that all fungal isolates belonged to phylum Ascomycota with the genus Penicillium representing 75% of the fungal isolates. P. janthinellum KTMT5 which was selected for further experiments showed significant anticancer activity against UMG87 cells with a calculated IC50 value of 44.23 μg/mL in the MTS assay, while the real time xCELLigence assay showed dose-dependent anticancer activity at 50 and 100 μg/mL. Metabolite profiling revealed the presence of several known metabolites in the crude extract of P. janthinellum KTMT5 and molecular networking showed the relationships among these metabolites.
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Wang G, Zhao J, Wang X, Wang T, Zhuang Y, Chu J, Zhang S, Noorman HJ. Quantitative metabolomics and metabolic flux analysis reveal impact of altered trehalose metabolism on metabolic phenotypes of Penicillium chrysogenum in aerobic glucose-limited chemostats. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.03.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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10
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Hao DC, Xiao PG. Deep in shadows: Epigenetic and epigenomic regulations of medicinal plants. CHINESE HERBAL MEDICINES 2018. [DOI: 10.1016/j.chmed.2018.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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Wang G, Wu B, Zhao J, Haringa C, Xia J, Chu J, Zhuang Y, Zhang S, Heijnen JJ, van Gulik W, Deshmukh AT, Noorman HJ. Power input effects on degeneration in prolonged penicillin chemostat cultures: A systems analysis at flux, residual glucose, metabolite, and transcript levels. Biotechnol Bioeng 2017; 115:114-125. [DOI: 10.1002/bit.26447] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 07/14/2017] [Accepted: 09/01/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Guan Wang
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology (ECUST); Shanghai People's Republic of China
| | - Baofeng Wu
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology (ECUST); Shanghai People's Republic of China
| | - Junfei Zhao
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology (ECUST); Shanghai People's Republic of China
| | - Cees Haringa
- Transport Phenomena, Chemical Engineering Department; Delft University of Technology; Delft The Netherlands
| | - Jianye Xia
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology (ECUST); Shanghai People's Republic of China
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology (ECUST); Shanghai People's Republic of China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology (ECUST); Shanghai People's Republic of China
| | - Siliang Zhang
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology (ECUST); Shanghai People's Republic of China
| | - Joseph J. Heijnen
- Cell Systems Engineering, Department of Biotechnology; Delft University of Technology; Delft The Netherlands
| | - Walter van Gulik
- Cell Systems Engineering, Department of Biotechnology; Delft University of Technology; Delft The Netherlands
| | | | - Henk J. Noorman
- DSM Biotechnology Center; Delft The Netherlands
- Bio Process Engineering, Department of Biotechnology; Delft University of Technology; Delft The Netherlands
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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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13
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Sandoval CM, Ayson M, Moss N, Lieu B, Jackson P, Gaucher SP, Horning T, Dahl RH, Denery JR, Abbott DA, Meadows AL. Use of pantothenate as a metabolic switch increases the genetic stability of farnesene producing Saccharomyces cerevisiae. Metab Eng 2014; 25:215-26. [DOI: 10.1016/j.ymben.2014.07.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 06/27/2014] [Accepted: 07/17/2014] [Indexed: 01/19/2023]
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Wang H, Pan Y, Hu P, Zhu Y, Li J, Jiang X, Liu G. The autophagy-related gene Acatg1 is involved in conidiation and cephalosporin production in Acremonium chrysogenum. Fungal Genet Biol 2014; 69:65-74. [DOI: 10.1016/j.fgb.2014.06.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 06/06/2014] [Accepted: 06/16/2014] [Indexed: 01/24/2023]
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Bajaj I, Veiga T, van Dissel D, Pronk JT, Daran JM. Functional characterization of a Penicillium chrysogenum mutanase gene induced upon co-cultivation with Bacillus subtilis. BMC Microbiol 2014; 14:114. [PMID: 24884713 PMCID: PMC4077275 DOI: 10.1186/1471-2180-14-114] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 04/17/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Microbial gene expression is strongly influenced by environmental growth conditions. Comparison of gene expression under different conditions is frequently used for functional analysis and to unravel regulatory networks, however, gene expression responses to co-cultivation with other microorganisms, a common occurrence in nature, is rarely studied under laboratory conditions. To explore cellular responses of the antibiotic-producing fungus Penicillium chrysogenum to prokaryotes, the present study investigates its transcriptional responses during co-cultivation with Bacillus subtilis. RESULTS Steady-state glucose-limited chemostats of P. chrysogenum grown under penillicin-non-producing conditions were inoculated with B. subtilis. Physiological and transcriptional responses of P. chrysogenum in the resulting mixed culture were monitored over 72 h. Under these conditions, B. subtilis outcompeted P. chrysogenum, as reflected by a three-fold increase of the B. subtilis population size and a two-fold reduction of the P. chrysogenum biomass concentration. Genes involved in the penicillin pathway and in synthesis of the penicillin precursors and side-chain were unresponsive to the presence of B. subtilis. Moreover, Penicillium polyketide synthase and nonribosomal peptide synthase genes were either not expressed or down-regulated. Among the highly responsive genes, two putative α-1,3 endoglucanase (mutanase) genes viz Pc12g07500 and Pc12g13330 were upregulated by more than 15-fold and 8-fold, respectively. Measurement of enzyme activity in the supernatant of mixed culture confirmed that the co-cultivation with B. subtilis induced mutanase production. Mutanase activity was neither observed in pure cultures of P. chrysogenum or B. subtilis, nor during exposure of P. chrysogenum to B. subtilis culture supernatants or heat-inactivated B. subtilis cells. However, mutanase production was observed in cultures of P. chrysogenum exposed to filter-sterilized supernatants of mixed cultures of P. chrysogenum and B. subtilis. Heterologous expression of Pc12g07500 and Pc12g13330 genes in Saccharomyces cerevisiae confirmed that Pc12g07500 encoded an active α-1,3 endoglucanase. CONCLUSION Time-course transcriptional profiling of P. chrysogenum revealed differentially expressed genes during co-cultivation with B. subtilis. Penicillin production was not induced under these conditions. However, induction of a newly characterized P. chrysogenum gene encoding α-1,3 endoglucanase may enhance the efficacy of fungal antibiotics by degrading bacterial exopolysaccharides.
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Affiliation(s)
- Ishwar Bajaj
- 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
| | - Tânia Veiga
- 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
| | - Dino van Dissel
- 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
| | - 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
- Platform for Green Synthetic Biology, P.O. Box 5057, 2600 GA Delft, the Netherlands
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Posch AE, Herwig C. Physiological description of multivariate interdependencies between process parameters, morphology and physiology during fed-batch penicillin production. Biotechnol Prog 2014; 30:689-99. [DOI: 10.1002/btpr.1901] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 01/30/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Andreas E. Posch
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses; Research Area Biochemical Engineering; Inst. of Chemical Engineering; Vienna University of Technology; Gumpendorfer Strasse 1a 1060 Vienna Austria
| | - Christoph Herwig
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses; Research Area Biochemical Engineering; Inst. of Chemical Engineering; Vienna University of Technology; Gumpendorfer Strasse 1a 1060 Vienna Austria
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17
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Lee HJ, Kim SW, Ryu JS, Lee CY, Ro HS. Isolation of a Variant Strain of Pleurotus eryngii and the Development of Specific DNA Markers to Identify the Variant Strain. MYCOBIOLOGY 2014; 42:46-51. [PMID: 24808734 PMCID: PMC4004947 DOI: 10.5941/myco.2014.42.1.46] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 01/23/2014] [Accepted: 01/23/2014] [Indexed: 06/03/2023]
Abstract
A degenerated strain of Pleurotus eryngii KNR2312 was isolated from a commercial farm. Random amplified polymorphic DNA analysis performed on the genomic DNA of the normal and degenerated strains of this species revealed differences in the DNA banding pattern. A unique DNA fragment (1.7 kbp), which appeared only in the degenerated strain, was isolated and sequenced. Comparing this sequence with the KNR2312 genomic sequence showed that the sequence of the degenerated strain comprised three DNA regions that originated from nine distinct scaffolds of the genomic sequence, suggesting that chromosome-level changes had occurred in the degenerated strain. Using the unique sequence, three sets of PCR primers were designed that targeted the full length, the 5' half, and the 3' half of the DNA. The primer sets P2-1 and P2-2 yielded 1.76 and 0.97 kbp PCR products, respectively, only in the case of the degenerated strain, whereas P2-3 generated a 0.8 kbp product in both the normal and the degenerated strains because its target region was intact in the normal strain as well. In the case of the P2-1 and P2-2 sets, the priming regions of the forward and reverse primers were located at distinct genomic scaffolds in the normal strain. These two primer sets specifically detected the degenerate strain of KNR2312 isolated from various mushrooms including 10 different strains of P. eryngii, four strains of P. ostreatus, and 11 other wild mushrooms.
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Affiliation(s)
- Hyun-Jun Lee
- Department of Microbiology and Research Institute of Life Sciences, Gyeongsang National University, Jinju 660-701, Korea
| | - Sang-Woo Kim
- Department of Microbiology and Research Institute of Life Sciences, Gyeongsang National University, Jinju 660-701, Korea
| | - Jae-San Ryu
- Gyeong Nam Agricultural Research and Extension Services, Jinju 660-360, Korea
| | | | - Hyeon-Su Ro
- Department of Microbiology and Research Institute of Life Sciences, Gyeongsang National University, Jinju 660-701, Korea
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Li L, Hu X, Xia Y, Xiao G, Zheng P, Wang C. Linkage of oxidative stress and mitochondrial dysfunctions to spontaneous culture degeneration in Aspergillus nidulans. Mol Cell Proteomics 2013; 13:449-61. [PMID: 24345786 DOI: 10.1074/mcp.m113.028480] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Filamentous fungi including mushrooms frequently and spontaneously degenerate during subsequent culture maintenance on artificial media, which shows the loss or reduction abilities of asexual sporulation, sexuality, fruiting, and production of secondary metabolites, thus leading to economic losses during mass production. To better understand the underlying mechanisms of fungal degeneration, the model fungus Aspergillus nidulans was employed in this study for comprehensive analyses. First, linkage of oxidative stress to culture degeneration was evident in A. nidulans. Taken together with the verifications of cell biology and biochemical data, a comparative mitochondrial proteome analysis revealed that, unlike the healthy wild type, a spontaneous fluffy sector culture of A. nidulans demonstrated the characteristics of mitochondrial dysfunctions. Relative to the wild type, the features of cytochrome c release, calcium overload and up-regulation of apoptosis inducing factors evident in sector mitochondria suggested a linkage of fungal degeneration to cell apoptosis. However, the sector culture could still be maintained for generations without the signs of growth arrest. Up-regulation of the heat shock protein chaperones, anti-apoptotic factors and DNA repair proteins in the sector could account for the compromise in cell death. The results of this study not only shed new lights on the mechanisms of spontaneous degeneration of fungal cultures but will also provide alternative biomarkers to monitor fungal culture degeneration.
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Affiliation(s)
- Lin Li
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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19
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Schmitz K, Peter V, Meinert S, Kornfeld G, Hardiman T, Wiechert W, Noack S. Simultaneous utilization of glucose and gluconate in Penicillium chrysogenum during overflow metabolism. Biotechnol Bioeng 2013; 110:3235-43. [PMID: 23775209 DOI: 10.1002/bit.24974] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 05/30/2013] [Accepted: 06/03/2013] [Indexed: 12/15/2022]
Abstract
The filamentous fungus Penicillium chrysogenum is one of the most important production organism for β-lactam antibiotics, especially penicillin. A specific feature of P. chrysogenum is the formation of gluconate as the primary overflow metabolite under non-limiting growth on glucose. Gluconate can be formed extracellularly by the enzyme glucose oxidase (GOD) that shows high activities under glucose excess conditions. Currently, it is assumed that under these conditions glucose is the preferred carbon substrate for P. chrysogenum and gluconate consumption first starts after glucose becomes limiting. Here, we specifically address this hypothesis by combining batch cultivation experiments on defined glucose media, time-dependent GOD activity measurements, and (13)C-tracer studies. Our data prove that both substrates are metabolized simultaneously independent from the actual glucose concentration and therefore suggest that no distinct mechanism of carbon catabolite repression exists for gluconate in P. chrysogenum. Moreover, gluconate consumption does not interfere with penicillin V production by repression of the penicillin genes. Finally, by following a model-driven approach the specific uptake rates for glucose and gluconate were quantified and found to be significantly higher for gluconate. In summary, our results show that P. chrysogenum metabolizes gluconate directly and at high rates making it an interesting alternative carbon source for production purposes.
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Affiliation(s)
- Katja Schmitz
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
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20
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Zheng P, Xia Y, Zhang S, Wang C. Genetics of Cordyceps and related fungi. Appl Microbiol Biotechnol 2013; 97:2797-804. [DOI: 10.1007/s00253-013-4771-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 02/09/2013] [Accepted: 02/11/2013] [Indexed: 12/29/2022]
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21
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Systematic applications of metabolomics in metabolic engineering. Metabolites 2012; 2:1090-122. [PMID: 24957776 PMCID: PMC3901235 DOI: 10.3390/metabo2041090] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 11/29/2012] [Accepted: 12/10/2012] [Indexed: 02/05/2023] Open
Abstract
The goals of metabolic engineering are well-served by the biological information provided by metabolomics: information on how the cell is currently using its biochemical resources is perhaps one of the best ways to inform strategies to engineer a cell to produce a target compound. Using the analysis of extracellular or intracellular levels of the target compound (or a few closely related molecules) to drive metabolic engineering is quite common. However, there is surprisingly little systematic use of metabolomics datasets, which simultaneously measure hundreds of metabolites rather than just a few, for that same purpose. Here, we review the most common systematic approaches to integrating metabolite data with metabolic engineering, with emphasis on existing efforts to use whole-metabolome datasets. We then review some of the most common approaches for computational modeling of cell-wide metabolism, including constraint-based models, and discuss current computational approaches that explicitly use metabolomics data. We conclude with discussion of the broader potential of computational approaches that systematically use metabolomics data to drive metabolic engineering.
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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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Veiga T, Solis-Escalante D, Romagnoli G, ten Pierick A, Hanemaaijer M, Deshmukh AT, Deshmuhk A, Wahl A, Pronk JT, Daran JM. Resolving phenylalanine metabolism sheds light on natural synthesis of penicillin G in Penicillium chrysogenum. EUKARYOTIC CELL 2012; 11:238-49. [PMID: 22158714 PMCID: PMC3272894 DOI: 10.1128/ec.05285-11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 12/02/2011] [Indexed: 11/20/2022]
Abstract
The industrial production of penicillin G by Penicillium chrysogenum requires the supplementation of the growth medium with the side chain precursor phenylacetate. The growth of P. chrysogenum with phenylalanine as the sole nitrogen source resulted in the extracellular production of phenylacetate and penicillin G. To analyze this natural pathway for penicillin G production, chemostat cultures were switched to [U-(13)C]phenylalanine as the nitrogen source. The quantification and modeling of the dynamics of labeled metabolites indicated that phenylalanine was (i) incorporated in nascent protein, (ii) transaminated to phenylpyruvate and further converted by oxidation or by decarboxylation, and (iii) hydroxylated to tyrosine and subsequently metabolized via the homogentisate pathway. The involvement of the homogentisate pathway was supported by the comparative transcriptome analysis of P. chrysogenum cultures grown with phenylalanine and with (NH(4))(2)SO(4) as the nitrogen source. This transcriptome analysis also enabled the identification of two putative 2-oxo acid decarboxylase genes (Pc13g9300 and Pc18g01490). cDNAs of both genes were cloned and expressed in the 2-oxo-acid-decarboxylase-free Saccharomyces cerevisiae strain CEN.PK711-7C (pdc1 pdc5 pdc6Δ aro10Δ thi3Δ). The introduction of Pc13g09300 restored the growth of this S. cerevisiae mutant on glucose and phenylalanine, thereby demonstrating that Pc13g09300 encodes a dual-substrate pyruvate and phenylpyruvate decarboxylase, which plays a key role in an Ehrlich-type pathway for the production of phenylacetate in P. chrysogenum. These results provide a basis for the metabolic engineering of P. chrysogenum for the production of the penicillin G side chain precursor phenylacetate.
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Affiliation(s)
- Tânia Veiga
- Industrial Microbiology Section, Department of Biotechnology, Delft University of Technology, Julianalaan 67, Delft, The Netherlands
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Douma RD, Deshmukh AT, de Jonge LP, de Jong BW, Seifar RM, Heijnen JJ, van Gulik WM. Novel insights in transport mechanisms and kinetics of phenylacetic acid and penicillin-G in Penicillium chrysogenum. Biotechnol Prog 2011; 28:337-48. [DOI: 10.1002/btpr.1503] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 11/24/2011] [Indexed: 11/06/2022]
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