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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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Gil-Durán C, Palma D, Marcano Y, Palacios JL, Martínez C, Rojas-Aedo JF, Levicán G, Vaca I, Chávez R. CRISPR/Cas9-Mediated Disruption of the pcz1 Gene and Its Impact on Growth, Development, and Penicillin Production in Penicillium rubens. J Fungi (Basel) 2023; 9:1010. [PMID: 37888266 PMCID: PMC10607824 DOI: 10.3390/jof9101010] [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: 08/04/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023] Open
Abstract
Penicillium rubens is a filamentous fungus of great biotechnological importance due to its role as an industrial producer of the antibiotic penicillin. However, despite its significance, our understanding of the regulatory mechanisms governing biological processes in this fungus is still limited. In fungi, zinc finger proteins containing a Zn(II)2Cys6 domain are particularly interesting regulators. Although the P. rubens genome harbors many genes encoding proteins with this domain, only two of them have been investigated thus far. In this study, we employed CRISPR-Cas9 technology to disrupt the pcz1 gene, which encodes a Zn(II)2Cys6 protein in P. rubens. The disruption of pcz1 resulted in a decrease in the production of penicillin in P. rubens. This decrease in penicillin production was accompanied by the downregulation of the expression of pcbAB, pcbC and penDE genes, which form the biosynthetic gene cluster responsible for penicillin production. Moreover, the disruption of pcz1 also impacts on asexual development, leading to decreased growth and conidiation, as well as enhanced conidial germination. Collectively, our results indicate that pcz1 acts as a positive regulator of penicillin production, growth, and conidiation, while functioning as a negative regulator of conidial germination in P. rubens. To the best of our knowledge, this is the first report involving a gene encoding a Zn(II)2Cys6 protein in the regulation of penicillin biosynthesis in P. rubens.
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Affiliation(s)
- Carlos Gil-Durán
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (C.G.-D.); (Y.M.); (J.F.R.-A.); (G.L.)
| | - Diego Palma
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile;
| | - Yudethzi Marcano
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (C.G.-D.); (Y.M.); (J.F.R.-A.); (G.L.)
| | - José-Luis Palacios
- Centro de Estudios en Ciencia y Tecnología de los Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (J.-L.P.); (C.M.)
| | - Claudio Martínez
- Centro de Estudios en Ciencia y Tecnología de los Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (J.-L.P.); (C.M.)
- Departamento de Ciencia y Tecnología de los Alimentos, Facultad Tecnológica, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile
| | - Juan F. Rojas-Aedo
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (C.G.-D.); (Y.M.); (J.F.R.-A.); (G.L.)
| | - Gloria Levicán
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (C.G.-D.); (Y.M.); (J.F.R.-A.); (G.L.)
| | - Inmaculada Vaca
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile;
| | - Renato Chávez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (C.G.-D.); (Y.M.); (J.F.R.-A.); (G.L.)
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Marcano Y, Montanares M, Gil-Durán C, González K, Levicán G, Vaca I, Chávez R. Pr laeA Affects the Production of Roquefortine C, Mycophenolic Acid, and Andrastin A in Penicillium roqueforti, but It Has Little Impact on Asexual Development. J Fungi (Basel) 2023; 9:954. [PMID: 37888210 PMCID: PMC10607316 DOI: 10.3390/jof9100954] [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: 07/28/2023] [Revised: 09/14/2023] [Accepted: 09/20/2023] [Indexed: 10/28/2023] Open
Abstract
The regulation of fungal specialized metabolism is a complex process involving various regulators. Among these regulators, LaeA, a methyltransferase protein originally discovered in Aspergillus spp., plays a crucial role. Although the role of LaeA in specialized metabolism has been studied in different fungi, its function in Penicillium roqueforti remains unknown. In this study, we employed CRISPR-Cas9 technology to disrupt the laeA gene in P. roqueforti (PrlaeA) aiming to investigate its impact on the production of the specialized metabolites roquefortine C, mycophenolic acid, and andrastin A, as well as on asexual development, because they are processes that occur in the same temporal stages within the physiology of the fungus. Our results demonstrate a substantial reduction in the production of the three metabolites upon disruption of PrlaeA, suggesting a positive regulatory role of LaeA in their biosynthesis. These findings were further supported by qRT-PCR analysis, which revealed significant downregulation in the expression of genes associated with the biosynthetic gene clusters (BGCs) responsible for producing roquefortine C, mycophenolic acid, and andrastin A in the ΔPrlaeA strains compared with the wild-type P. roqueforti. Regarding asexual development, the disruption of PrlaeA led to a slight decrease in colony growth rate, while conidiation and conidial germination remained unaffected. Taken together, our results suggest that LaeA positively regulates the expression of the analyzed BGCs and the production of their corresponding metabolites in P. roqueforti, but it has little impact on asexual development.
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Affiliation(s)
- Yudethzi Marcano
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (Y.M.); (C.G.-D.); (K.G.); (G.L.)
| | - Mariana Montanares
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile;
| | - Carlos Gil-Durán
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (Y.M.); (C.G.-D.); (K.G.); (G.L.)
| | - Kathia González
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (Y.M.); (C.G.-D.); (K.G.); (G.L.)
| | - Gloria Levicán
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (Y.M.); (C.G.-D.); (K.G.); (G.L.)
| | - Inmaculada Vaca
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile;
| | - Renato Chávez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (Y.M.); (C.G.-D.); (K.G.); (G.L.)
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Nègre D, Larhlimi A, Bertrand S. Reconciliation and evolution of Penicillium rubens genome-scale metabolic networks-What about specialised metabolism? PLoS One 2023; 18:e0289757. [PMID: 37647283 PMCID: PMC10468094 DOI: 10.1371/journal.pone.0289757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/24/2023] [Indexed: 09/01/2023] Open
Abstract
In recent years, genome sequencing of filamentous fungi has revealed a high proportion of specialised metabolites with growing pharmaceutical interest. However, detecting such metabolites through in silico genome analysis does not necessarily guarantee their expression under laboratory conditions. However, one plausible strategy for enabling their production lies in modifying the growth conditions. Devising a comprehensive experimental design testing in different culture environments is time-consuming and expensive. Therefore, using in silico modelling as a preliminary step, such as Genome-Scale Metabolic Network (GSMN), represents a promising approach to predicting and understanding the observed specialised metabolite production in a given organism. To address these questions, we reconstructed a new high-quality GSMN for the Penicillium rubens Wisconsin 54-1255 strain, a commonly used model organism. Our reconstruction, iPrub22, adheres to current convention standards and quality criteria, incorporating updated functional annotations, orthology searches with different GSMN templates, data from previous reconstructions, and manual curation steps targeting primary and specialised metabolites. With a MEMOTE score of 74% and a metabolic coverage of 45%, iPrub22 includes 5,192 unique metabolites interconnected by 5,919 reactions, of which 5,033 are supported by at least one genomic sequence. Of the metabolites present in iPrub22, 13% are categorised as belonging to specialised metabolism. While our high-quality GSMN provides a valuable resource for investigating known phenotypes expressed in P. rubens, our analysis identifies bottlenecks related, in particular, to the definition of what is a specialised metabolite, which requires consensus within the scientific community. It also points out the necessity of accessible, standardised and exhaustive databases of specialised metabolites. These questions must be addressed to fully unlock the potential of natural product production in P. rubens and other filamentous fungi. Our work represents a foundational step towards the objective of rationalising the production of natural products through GSMN modelling.
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Affiliation(s)
- Delphine Nègre
- Nantes Université, Institut des Substances et Organismes de la Mer, ISOMer, Nantes, France
- Nantes Université, École Centrale Nantes, CNRS, Nantes, France
| | | | - Samuel Bertrand
- Nantes Université, Institut des Substances et Organismes de la Mer, ISOMer, Nantes, France
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Correia J, Borges A, Simões M, Simões LC. Beyond Penicillin: The Potential of Filamentous Fungi for Drug Discovery in the Age of Antibiotic Resistance. Antibiotics (Basel) 2023; 12:1250. [PMID: 37627670 PMCID: PMC10451904 DOI: 10.3390/antibiotics12081250] [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: 07/03/2023] [Revised: 07/24/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Antibiotics are a staple in current medicine for the therapy of infectious diseases. However, their extensive use and misuse, combined with the high adaptability of bacteria, has dangerously increased the incidence of multi-drug-resistant (MDR) bacteria. This makes the treatment of infections challenging, especially when MDR bacteria form biofilms. The most recent antibiotics entering the market have very similar modes of action to the existing ones, so bacteria rapidly catch up to those as well. As such, it is very important to adopt effective measures to avoid the development of antibiotic resistance by pathogenic bacteria, but also to perform bioprospecting of new molecules from diverse sources to expand the arsenal of drugs that are available to fight these infectious bacteria. Filamentous fungi have a large and vastly unexplored secondary metabolome and are rich in bioactive molecules that can be potential novel antimicrobial drugs. Their production can be challenging, as the associated biosynthetic pathways may not be active under standard culture conditions. New techniques involving metabolic and genetic engineering can help boost antibiotic production. This study aims to review the bioprospection of fungi to produce new drugs to face the growing problem of MDR bacteria and biofilm-associated infections.
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Affiliation(s)
- João Correia
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, Department of Chemical Engineering, University of Porto, 4200-465 Porto, Portugal; (J.C.); (A.B.)
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal
| | - Anabela Borges
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, Department of Chemical Engineering, University of Porto, 4200-465 Porto, Portugal; (J.C.); (A.B.)
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal
| | - Manuel Simões
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, Department of Chemical Engineering, University of Porto, 4200-465 Porto, Portugal; (J.C.); (A.B.)
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal
| | - Lúcia C. Simões
- CEB—Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal;
- LABBELS—Associate Laboratory in Biotechnology, Bioengineering and Microelectromechanical Systems, 4710-057 Braga, Portugal
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6
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Zhgun AA. Fungal BGCs for Production of Secondary Metabolites: Main Types, Central Roles in Strain Improvement, and Regulation According to the Piano Principle. Int J Mol Sci 2023; 24:11184. [PMID: 37446362 PMCID: PMC10342363 DOI: 10.3390/ijms241311184] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 06/28/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Filamentous fungi are one of the most important producers of secondary metabolites. Some of them can have a toxic effect on the human body, leading to diseases. On the other hand, they are widely used as pharmaceutically significant drugs, such as antibiotics, statins, and immunosuppressants. A single fungus species in response to various signals can produce 100 or more secondary metabolites. Such signaling is possible due to the coordinated regulation of several dozen biosynthetic gene clusters (BGCs), which are mosaically localized in different regions of fungal chromosomes. Their regulation includes several levels, from pathway-specific regulators, whose genes are localized inside BGCs, to global regulators of the cell (taking into account changes in pH, carbon consumption, etc.) and global regulators of secondary metabolism (affecting epigenetic changes driven by velvet family proteins, LaeA, etc.). In addition, various low-molecular-weight substances can have a mediating effect on such regulatory processes. This review is devoted to a critical analysis of the available data on the "turning on" and "off" of the biosynthesis of secondary metabolites in response to signals in filamentous fungi. To describe the ongoing processes, the model of "piano regulation" is proposed, whereby pressing a certain key (signal) leads to the extraction of a certain sound from the "musical instrument of the fungus cell", which is expressed in the production of a specific secondary metabolite.
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Affiliation(s)
- Alexander A Zhgun
- Group of Fungal Genetic Engineering, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Leninsky Prosp. 33-2, 119071 Moscow, Russia
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Kosalková K, Barreiro C, Sánchez-Orejas IC, Cueto L, García-Estrada C. Biotechnological Fungal Platforms for the Production of Biosynthetic Cannabinoids. J Fungi (Basel) 2023; 9:jof9020234. [PMID: 36836348 PMCID: PMC9963667 DOI: 10.3390/jof9020234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/07/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
Cannabinoids are bioactive meroterpenoids comprising prenylated polyketide molecules that can modulate a wide range of physiological processes. Cannabinoids have been shown to possess various medical/therapeutic effects, such as anti-convulsive, anti-anxiety, anti-psychotic, antinausea, and anti-microbial properties. The increasing interest in their beneficial effects and application as clinically useful drugs has promoted the development of heterologous biosynthetic platforms for the industrial production of these compounds. This approach can help circumvent the drawbacks associated with extraction from naturally occurring plants or chemical synthesis. In this review, we provide an overview of the fungal platforms developed by genetic engineering for the biosynthetic production of cannabinoids. Different yeast species, such as Komagataella phaffii (formerly P. pastoris) and Saccharomyces cerevisiae, have been genetically modified to include the cannabinoid biosynthetic pathway and to improve metabolic fluxes in order to increase cannabinoid titers. In addition, we engineered the filamentous fungus Penicillium chrysogenum for the first time as a host microorganism for the production of Δ9-tetrahydrocannabinolic acid from intermediates (cannabigerolic acid and olivetolic acid), thereby showing the potential of filamentous fungi as alternative platforms for cannabinoid biosynthesis upon optimization.
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Affiliation(s)
- Katarina Kosalková
- INBIOTEC (Instituto de Biotecnología de León), Av. Real 1, 24006 León, Spain
| | - Carlos Barreiro
- INBIOTEC (Instituto de Biotecnología de León), Av. Real 1, 24006 León, Spain
- Área de Bioquímica y Biología Molecular, Departamento de Biología Molecular, Campus de Vegazana, Universidad de León, 24007 León, Spain
| | | | - Laura Cueto
- INBIOTEC (Instituto de Biotecnología de León), Av. Real 1, 24006 León, Spain
| | - Carlos García-Estrada
- INBIOTEC (Instituto de Biotecnología de León), Av. Real 1, 24006 León, Spain
- Departamento de Ciencias Biomédicas, Campus de Vegazana, Universidad de León, 24007 León, Spain
- Correspondence: ; Tel.: +34-987-293-693
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García-Calvo L, Rodríguez-Castro R, Ullán RV, Albillos SM, Fernández-Aguado M, Vicente CM, Degnes KF, Sletta H, Barreiro C. Penicillium chrysogenum as a fungal factory for feruloyl esterases. Appl Microbiol Biotechnol 2023; 107:691-717. [PMID: 36595038 DOI: 10.1007/s00253-022-12335-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 12/05/2022] [Accepted: 12/08/2022] [Indexed: 01/04/2023]
Abstract
Plant biomass is a promising substrate for biorefinery, as well as a source of bioactive compounds, platform chemicals, and precursors with multiple industrial applications. These applications depend on the hydrolysis of its recalcitrant structure. However, the effective biological degradation of plant cell walls requires several enzymatic groups acting synergistically, and novel enzymes are needed in order to achieve profitable industrial hydrolysis processes. In the present work, a feruloyl esterase (FAE) activity screening of Penicillium spp. strains revealed a promising candidate (Penicillium rubens Wisconsin 54-1255; previously Penicillium chrysogenum), where two FAE-ORFs were identified and subsequently overexpressed. Enzyme extracts were analyzed, confirming the presence of FAE activity in the respective gene products (PrFaeA and PrFaeB). PrFaeB-enriched enzyme extracts were used to determine the FAE activity optima (pH 5.0 and 50-55 °C) and perform proteome analysis by means of MALDI-TOF/TOF mass spectrometry. The studies were completed with the determination of other lignocellulolytic activities, an untargeted metabolite analysis, and upscaled FAE production in stirred tank reactors. The findings described in this work present P. rubens as a promising lignocellulolytic enzyme producer. KEY POINTS: • Two Penicillium rubens ORFs were first confirmed to have feruloyl esterase activity. • Overexpression of the ORFs produced a novel P. rubens strain with improved activity. • The first in-depth proteomic study of a P. rubens lignocellulolytic extract is shown.
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Affiliation(s)
- Laura García-Calvo
- INBIOTEC (Instituto de Biotecnología de León), Avda. Real 1 - Parque Científico de León, 24006, León, Spain
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| | - Raquel Rodríguez-Castro
- INBIOTEC (Instituto de Biotecnología de León), Avda. Real 1 - Parque Científico de León, 24006, León, Spain
| | - Ricardo V Ullán
- INBIOTEC (Instituto de Biotecnología de León), Avda. Real 1 - Parque Científico de León, 24006, León, Spain.
- mAbxience, Upstream Production, Parque Tecnológico de León, Julia Morros, S/N, Armunia, 24009, 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, 09001, Burgos, Spain
| | - Marta Fernández-Aguado
- INBIOTEC (Instituto de Biotecnología de León), Avda. Real 1 - Parque Científico de León, 24006, León, Spain
| | - Cláudia M Vicente
- INBIOTEC (Instituto de Biotecnología de León), Avda. Real 1 - Parque Científico de León, 24006, León, Spain
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077, Toulouse, France
| | - Kristin F Degnes
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Richard Birkelands Vei 3 B, 7034, Trondheim, Norway
| | - Håvard Sletta
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Richard Birkelands Vei 3 B, 7034, Trondheim, Norway
| | - Carlos Barreiro
- Área de Bioquímica Y Biología Molecular, Departamento de Biología Molecular, Universidad de León, Campus de Vegazana, 24007, León, Spain.
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Interconnected Set of Enzymes Provide Lysine Biosynthetic Intermediates and Ornithine Derivatives as Key Precursors for the Biosynthesis of Bioactive Secondary Metabolites. Antibiotics (Basel) 2023; 12:antibiotics12010159. [PMID: 36671360 PMCID: PMC9854754 DOI: 10.3390/antibiotics12010159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Bacteria, filamentous fungi, and plants synthesize thousands of secondary metabolites with important biological and pharmacological activities. The biosynthesis of these metabolites is performed by networks of complex enzymes such as non-ribosomal peptide synthetases, polyketide synthases, and terpenoid biosynthetic enzymes. The efficient production of these metabolites is dependent upon the supply of precursors that arise from primary metabolism. In the last decades, an impressive array of biosynthetic enzymes that provide specific precursors and intermediates leading to secondary metabolites biosynthesis has been reported. Suitable knowledge of the elaborated pathways that synthesize these precursors or intermediates is essential for advancing chemical biology and the production of natural or semisynthetic biological products. Two of the more prolific routes that provide key precursors in the biosynthesis of antitumor, immunosuppressant, antifungal, or antibacterial compounds are the lysine and ornithine pathways, which are involved in the biosynthesis of β-lactams and other non-ribosomal peptides, and bacterial and fungal siderophores. Detailed analysis of the molecular genetics and biochemistry of the enzyme system shows that they are formed by closely related components. Particularly the focus of this study is on molecular genetics and the enzymatic steps that lead to the formation of intermediates of the lysine pathway, such as α-aminoadipic acid, saccharopine, pipecolic acid, and related compounds, and of ornithine-derived molecules, such as N5-Acetyl-N5-Hydroxyornithine and N5-anhydromevalonyl-N5-hydroxyornithine, which are precursors of siderophores. We provide evidence that shows interesting functional relationships between the genes encoding the enzymes that synthesize these products. This information will contribute to a better understanding of the possibilities of advancing the industrial applications of synthetic biology.
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Characterization of Microbial Diversity in Decayed Wood from a Spanish Forest: An Environmental Source of Industrially Relevant Microorganisms. Microorganisms 2022; 10:microorganisms10061249. [PMID: 35744767 PMCID: PMC9227542 DOI: 10.3390/microorganisms10061249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/20/2022] [Accepted: 06/16/2022] [Indexed: 11/16/2022] Open
Abstract
Rotting wood is inhabited by a large diversity of bacteria, fungi, and insects with complex environmental relationships. The aim of this work was to study the composition of the microbiota (bacteria and fungi) in decaying wood from a northwest Spanish forest as a source of industrially relevant microorganisms. The analyzed forest is situated in a well-defined biogeographic area combining Mediterranean and temperate macrobioclimates. Bacterial diversity, determined by metagenome analyses, was higher than fungal heterogeneity. However, a total of 194 different cultivable bacterial isolates (mainly Bacillaceae, Streptomycetaceae, Paenibacillaceae, and Microbacteriaceae) were obtained, in contrast to 343 fungal strains (mainly Aspergillaceae, Hypocreaceae, and Coniochaetaceae). Isolates traditionally known as secondary metabolite producers, such as Actinobacteria and members of the Penicillium genus, were screened for their antimicrobial activity by the detection of antibiotic biosynthetic clusters and competitive bioassays against fungi involved in wood decay. In addition, the ability of Penicillium isolates to degrade cellulose and release ferulic acid from wood was also examined. These results present decaying wood as an ecologically rich niche and a promising source of biotechnologically interesting microorganisms.
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Lv N, Zhang L, Yang Z, Wang H, Yang N, Li H. Label-free biological sample detection and non-contact separation system based on microfluidic chip. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:063104. [PMID: 35778042 DOI: 10.1063/5.0086109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
The detection and separation of biological samples are of great significance for achieving accurate diagnoses and state assessments. Currently, the detection and separation of cells mostly adopt labeling methods, which will undoubtedly affect the original physiological state and functions of cells. Therefore, in this study, a label-free cell detection method based on microfluidic chips is proposed. By measuring the scattering of cells to identify cells and then using optical tweezers to separate the target cells, the whole process without any labeling and physical contact could realize automatic cell identification and separation. Different concentrations of 15 µm polystyrene microspheres and yeast mixed solution are used as samples for detection and separation. The detection accuracy is over 90%, and the separation accuracy is over 73%.
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Affiliation(s)
- Ning Lv
- School of Mechanical Engineering, Xian Jiaotong University, Xian, Shannxi 710049, China
| | - Lu Zhang
- School of Mechanical Engineering, Xian Jiaotong University, Xian, Shannxi 710049, China
| | - Zewen Yang
- School of Mechanical Engineering, Xian Jiaotong University, Xian, Shannxi 710049, China
| | - Huijun Wang
- School of Mechanical Engineering, Xian Jiaotong University, Xian, Shannxi 710049, China
| | - Nan Yang
- School of Mechanical Engineering, Xian Jiaotong University, Xian, Shannxi 710049, China
| | - Hao Li
- School of Mechanical Engineering, Xian Jiaotong University, Xian, Shannxi 710049, China
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12
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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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13
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Kück U, Dahlmann TA. The Confusion in Renaming Species: Penicillium chrysogenum and Penicillium rubens. Microbiol Resour Announc 2021; 10:e0046421. [PMID: 34854731 PMCID: PMC8638606 DOI: 10.1128/mra.00464-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Ulrich Kück
- Allgemeine und Molekulare Botanik, Ruhr-Universität, Bochum, Germany
| | - Tim A. Dahlmann
- Allgemeine und Molekulare Botanik, Ruhr-Universität, Bochum, Germany
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14
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Ameen F, AlNAdhari S, Yassin MA, Al-Sabri A, Almansob A, Alqahtani N, Stephenson SL. Desert soil fungi isolated from Saudi Arabia: cultivable fungal community and biochemical production. Saudi J Biol Sci 2021; 29:2409-2420. [PMID: 35531195 PMCID: PMC9072920 DOI: 10.1016/j.sjbs.2021.12.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/20/2021] [Accepted: 12/05/2021] [Indexed: 02/08/2023] Open
Abstract
Desert soils harbor fungi that have survived under highly stressed conditions of high temperature and little available moisture. This study was designed to survey the communities of cultivable fungi in the desert soils of the Arabian Peninsula and to screen the fungi for the potentially valuable antioxidants (flavonoids, phenols, saponins, steroids, tannins, terpenoids, and alkaloids) and enzymes (cellulase, laccase, lipase, protease, amylase, and chitinase). Desert soil was sampled at 30 localities representing different areas of Saudi Arabia and studied for physico-chemical soil properties. Five types of soil texture (sand, loamy sand, sandy loam, silty loam, and sandy clay loam) were observed. A total of 25 saprotrophic species was identified molecularly from 68 isolates. Our survey revealed 13 culturable fungal species that have not been reported previously from Arabian desert soils and six more species not reported from Saudi Arabian desert soils. The most commonly recorded genera were Aspergillus (isolated from 20 localities) and Penicillium (6 localities). The measurements of biochemicals revealed that antioxidants were produced by 49 and enzymes by 52 isolates; only six isolates did not produce any biochemicals. The highest biochemical activity was observed for the isolates Fusarium brachygibbosum and A. phoenicis. Other active isolates were A. proliferans and P. chrysogenum. The same species, for instance, A. niger had isolates of both high and low biochemical activities. Principal component analysis gave a tentative indication of a relationship between the biochemical activity of fungi isolated from soil and soil texture variables namely the content of silt, clay and sand. However, any generalizable relation between soil properties and fungal biochemical activities cannot be suggested. Each fungal isolate is probable to produce several antioxidants and enzymes, as shown by the correlation within the compound groups. Desert soil warrants further research as a promising source of biochemicals.
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15
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Worldwide Clinical Demand for Antibiotics: Is It a Real Countdown? METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2296:3-15. [PMID: 33977439 DOI: 10.1007/978-1-0716-1358-0_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Antibiotics are antimicrobial agents primarily produced by certain bacteria and fungi. These drugs are some of the biological weapons used by the producers to survive in their dense and multispecies communities where the resources could be scarce. Thus, the microorganisms, as antibiotic producers, also have the skills to avoid the antibiotic affect from immemorial time. However, the antibiotic resistance is a current global health threat because of the overuse, abuse, or use of antibiotics. Nowadays, resistance to all the antibiotic classes has emerged, which results in 700,000 annual deaths due to the drug-resistant diseases, and forecasts are dramatic for the coming years. This chapter reviews the evolution of the antibiotics discovery, the worldwide antibiotics resistances threat, their economical and clinical impact, as well as how the academia and the enterprises are facing the need of new antibiotics discovery or antimicrobial therapies implementation.
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16
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Chen Y, Zheng S, Zhang G, Luo J, Liu J, Peng X. Chemical, microbial, and metabolic analysis of Taisui cultured in honey solution. Food Sci Nutr 2021; 9:2158-2168. [PMID: 33841832 PMCID: PMC8020961 DOI: 10.1002/fsn3.2185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/27/2021] [Accepted: 02/06/2021] [Indexed: 11/17/2022] Open
Abstract
Taisui, a special substance occasionally found in China, can now be artificially cultured. In order to evaluate the safety of an artificially cultured Taisui (acTS) and develop it into fermented, functional food or oral liquid, the macronutrients, trace elements, microbial community, and extracellular metabolites of Taisui have been investigated in this study. Results showed that the concentrations of total carbohydrates, protein, fat, total ash, and moisture of wet acTS were 2.13 g/100 g, 0.13 g/100 g, 0.07 g/100 g, 0.04 g/100 g, and 88.3%, respectively. The concentrations of top three trace elements of K, Ca, and P, are 1,424.92 mg/kg, 159.96 mg/kg, and 67.89 mg/kg, respectively. Proteobacteria, Euryarchaeota, and Ascomycota were the dominant phyla of bacteria, archaea, and fungi, respectively. Uncultured_bacterium_f_Anaerolineaceae, Alcaligenes, and Ochrobactrum were the three most abundant genera of bacteria; Methanosaeta, Methanosphaera, and Natronomonas, the most abundant genera of archaea; Zygosaccharomyces, Mortierella, and Fusarium, the most abundant genera of fungi. There were 311 metabolites increased in acTS. Most of the metabolites are beneficial to human. These metabolites can be contributed to microbes in acTS. In conclusion, acTS is not a good source of macronutrients and of trace elements, while the safeness of some microorganisms in acTS is also unknown. Nevertheless, it still provides some probiotics and beneficial metabolites for human. It is thus possible to develop acTS into foods when the safety of each microorganism is proved.
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Affiliation(s)
- Yunjing Chen
- Department of Food Science and EngineeringJinan UniversityGuangzhou510632China
| | - Shuxiu Zheng
- Department of Food Science and EngineeringJinan UniversityGuangzhou510632China
| | - Guangwen Zhang
- Department of Food Science and EngineeringJinan UniversityGuangzhou510632China
| | - Jianming Luo
- Department of Food Science and EngineeringJinan UniversityGuangzhou510632China
| | - Junsheng Liu
- Department of Food Science and EngineeringJinan UniversityGuangzhou510632China
| | - Xichun Peng
- Department of Food Science and EngineeringJinan UniversityGuangzhou510632China
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17
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Fizeșan I, Rusu ME, Georgiu C, Pop A, Ștefan MG, Muntean DM, Mirel S, Vostinaru O, Kiss B, Popa DS. Antitussive, Antioxidant, and Anti-Inflammatory Effects of a Walnut ( Juglans regia L.) Septum Extract Rich in Bioactive Compounds. Antioxidants (Basel) 2021; 10:119. [PMID: 33467612 PMCID: PMC7830861 DOI: 10.3390/antiox10010119] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 02/07/2023] Open
Abstract
The antitussive, antioxidant, and anti-inflammatory effects of a walnut (Juglans regia L.) septum extract (WSE), rich in bioactive compounds were investigated using the citric acid aerosol-induced cough experimental model in rodents. Wistar male rats were treated orally for three days with distilled water (control), codeine (reference), and WSE in graded doses. On the third day, all rats were exposed to citric acid aerosols, the number of coughs being recorded. Each animal was sacrificed after exposure, and blood and lung tissue samples were collected for histopathological analysis and the assessment of oxidative stress and inflammatory biomarkers. The results of the experiment showed a significant antitussive effect of WSE, superior to codeine. This activity could be due to cellular protective effect and anti-inflammatory effect via the stimulation of the antioxidant enzyme system and the decrease of IL-6 and CXC-R1 concentration in the lung tissue of WSE-treated animals. The antioxidant and anti-inflammatory effects of WSE were confirmed by biochemical assays and histopathological analysis. This is the first scientific study reporting the antitussive effect of walnut septum, a new potential source of non-opioid antitussive drug candidates, and a valuable bioactive by-product that could be used in the treatment of respiratory diseases.
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Affiliation(s)
- Ionel Fizeșan
- Department of Toxicology, Faculty of Pharmacy, Iuliu Hatieganu University of Medicine and Pharmacy, 8 Victor Babes, 400012 Cluj-Napoca, Romania; (I.F.); (A.P.); (M.-G.Ș.); (B.K.); (D.-S.P.)
| | - Marius Emil Rusu
- Department of Pharmaceutical Technology and Biopharmaceutics, Faculty of Pharmacy, Iuliu Hatieganu University of Medicine and Pharmacy, 8 Victor Babes, 400012 Cluj-Napoca, Romania; (M.E.R.); (D.-M.M.)
| | - Carmen Georgiu
- Department of Pathological Anatomy, Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 8 Victor Babes, 400012 Cluj-Napoca, Romania
| | - Anca Pop
- Department of Toxicology, Faculty of Pharmacy, Iuliu Hatieganu University of Medicine and Pharmacy, 8 Victor Babes, 400012 Cluj-Napoca, Romania; (I.F.); (A.P.); (M.-G.Ș.); (B.K.); (D.-S.P.)
| | - Maria-Georgia Ștefan
- Department of Toxicology, Faculty of Pharmacy, Iuliu Hatieganu University of Medicine and Pharmacy, 8 Victor Babes, 400012 Cluj-Napoca, Romania; (I.F.); (A.P.); (M.-G.Ș.); (B.K.); (D.-S.P.)
| | - Dana-Maria Muntean
- Department of Pharmaceutical Technology and Biopharmaceutics, Faculty of Pharmacy, Iuliu Hatieganu University of Medicine and Pharmacy, 8 Victor Babes, 400012 Cluj-Napoca, Romania; (M.E.R.); (D.-M.M.)
| | - Simona Mirel
- Department of Medical Devices, Faculty of Pharmacy, Iuliu Hatieganu University of Medicine and Pharmacy, 8 Victor Babes, 400012 Cluj-Napoca, Romania;
| | - Oliviu Vostinaru
- Department of Pharmacology, Physiology and Physiopathology, Faculty of Pharmacy, Iuliu Hatieganu University of Medicine and Pharmacy, 8 Victor Babes, 400012 Cluj-Napoca, Romania
| | - Béla Kiss
- Department of Toxicology, Faculty of Pharmacy, Iuliu Hatieganu University of Medicine and Pharmacy, 8 Victor Babes, 400012 Cluj-Napoca, Romania; (I.F.); (A.P.); (M.-G.Ș.); (B.K.); (D.-S.P.)
| | - Daniela-Saveta Popa
- Department of Toxicology, Faculty of Pharmacy, Iuliu Hatieganu University of Medicine and Pharmacy, 8 Victor Babes, 400012 Cluj-Napoca, Romania; (I.F.); (A.P.); (M.-G.Ș.); (B.K.); (D.-S.P.)
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