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Gambarini V, Drost CJ, Kingsbury JM, Weaver L, Pantos O, Handley KM, Lear G. Uncoupled: investigating the lack of correlation between the transcription of putative plastic-degrading genes in the global ocean microbiome and marine plastic pollution. ENVIRONMENTAL MICROBIOME 2024; 19:34. [PMID: 38750536 PMCID: PMC11097532 DOI: 10.1186/s40793-024-00575-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 05/01/2024] [Indexed: 05/18/2024]
Abstract
BACKGROUND Plastic pollution is a severe threat to marine ecosystems. While some microbial enzymes can degrade certain plastics, the ability of the global ocean microbiome to break down diverse environmental plastics remains limited. We employed metatranscriptomic data from an international ocean survey to explore global and regional patterns in microbial plastic degradation potential. RESULTS On a global oceanic scale, we found no significant correlation between levels of plastic pollution and the expression of genes encoding enzymes putatively identified as capable of plastic degradation. Even when looking at different regional scales, ocean depth layers, or plastic types, we found no strong or even moderate correlation between plastic pollution and relative abundances of transcripts for enzymes with presumed plastic biodegradation potential. Our data, however, indicate that microorganisms in the Southern Ocean show a higher potential for plastic degradation, making them more appealing candidates for bioprospecting novel plastic-degrading enzymes. CONCLUSION Our research contributes to understanding the complex global relationship between plastic pollution and microbial plastic degradation potential. We reveal that the transcription of putative plastic-degrading genes in the global ocean microbiome does not correlate to marine plastic pollution, highlighting the ongoing danger that plastic poses to marine environments threatened by plastic pollution.
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Affiliation(s)
- Victor Gambarini
- School of Biological Sciences, University of Auckland, 3a Symonds Street, Auckland, 1010, New Zealand
- Centre for eResearch, University of Auckland, 23 Symonds Street, Auckland, 1010, New Zealand
| | - Cornelis J Drost
- Centre for eResearch, University of Auckland, 23 Symonds Street, Auckland, 1010, New Zealand
| | - Joanne M Kingsbury
- The Institute of Environmental Science and Research, 27 Creyke Road, Ilam, Christchurch, 8041, New Zealand
| | - Louise Weaver
- The Institute of Environmental Science and Research, 27 Creyke Road, Ilam, Christchurch, 8041, New Zealand
| | - Olga Pantos
- The Institute of Environmental Science and Research, 27 Creyke Road, Ilam, Christchurch, 8041, New Zealand
| | - Kim M Handley
- School of Biological Sciences, University of Auckland, 3a Symonds Street, Auckland, 1010, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, 3a Symonds Street, Auckland, 1010, New Zealand.
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2
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Nguyen LAC, Mori M, Yasuda Y, Galipon J. Functional Consequences of Shifting Transcript Boundaries in Glucose Starvation. Mol Cell Biol 2023; 43:611-628. [PMID: 37937348 PMCID: PMC10761120 DOI: 10.1080/10985549.2023.2270406] [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: 07/11/2023] [Accepted: 10/10/2023] [Indexed: 11/09/2023] Open
Abstract
Glucose is a major source of carbon and essential for the survival of many organisms, ranging from yeast to human. A sudden 60-fold reduction of glucose in exponentially growing fission yeast induces transcriptome-wide changes in gene expression. This regulation is multilayered, and the boundaries of transcripts are known to vary, with functional consequences at the protein level. By combining direct RNA sequencing with 5'-CAGE and short-read sequencing, we accurately defined the 5'- and 3'-ends of transcripts that are both poly(A) tailed and 5'-capped in glucose starvation, followed by proteome analysis. Our results confirm previous experimentally validated loci with alternative isoforms and reveal several transcriptome-wide patterns. First, we show that sense-antisense gene pairs are more strongly anticorrelated when a time lag is taken into account. Second, we show that the glucose starvation response initially elicits a shortening of 3'-UTRs and poly(A) tails, followed by a shortening of the 5'-UTRs at later time points. These result in domain gains and losses in proteins involved in the stress response. Finally, the relatively poor overlap both between differentially expressed genes (DEGs), differential transcript usage events (DTUs), and differentially detected proteins (DDPs) highlight the need for further study on post-transcriptional regulation mechanisms in glucose starvation.
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Affiliation(s)
- Lan Anh Catherine Nguyen
- Institute for Advanced Biosciences, Keio University, Yamagata, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Kanagawa, Fujisawa, Japan
| | - Masaru Mori
- Institute for Advanced Biosciences, Keio University, Yamagata, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Kanagawa, Fujisawa, Japan
- Institute of Innovation for Future Society, Nagoya University, Aichi, Nagoya, Japan
| | - Yuji Yasuda
- Institute for Advanced Biosciences, Keio University, Yamagata, Tsuruoka, Japan
- Faculty of Environment and Information Studies, Keio University, Kanagawa, Fujisawa, Japan
| | - Josephine Galipon
- Institute for Advanced Biosciences, Keio University, Yamagata, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Kanagawa, Fujisawa, Japan
- Graduate School of Science and Engineering, Yamagata University, Yamagata, Yonezawa, Japan
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3
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Scott M, Hwa T. Shaping bacterial gene expression by physiological and proteome allocation constraints. Nat Rev Microbiol 2023; 21:327-342. [PMID: 36376406 PMCID: PMC10121745 DOI: 10.1038/s41579-022-00818-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2022] [Indexed: 11/16/2022]
Abstract
Networks of molecular regulators are often the primary objects of focus in the study of gene regulation, with the machinery of protein synthesis tacitly relegated to the background. Shifting focus to the constraints imposed by the allocation of protein synthesis flux reveals surprising ways in which the actions of molecular regulators are shaped by physiological demands. Using carbon catabolite repression as a case study, we describe how physiological constraints are sensed through metabolic fluxes and how flux-controlled regulation gives rise to simple empirical relations between protein levels and the rate of cell growth.
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Affiliation(s)
- Matthew Scott
- Department of Applied Mathematics, University of Waterloo, Waterloo, ON, Canada.
| | - Terence Hwa
- Department of Physics, University of California at San Diego, La Jolla, CA, USA.
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4
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Mohamed NZ, Shaban L, Safan S, El-Sayed ASA. Physiological and metabolic traits of Taxol biosynthesis of endophytic fungi inhabiting plants: Plant-microbial crosstalk, and epigenetic regulators. Microbiol Res 2023; 272:127385. [PMID: 37141853 DOI: 10.1016/j.micres.2023.127385] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 04/08/2023] [Accepted: 04/09/2023] [Indexed: 05/06/2023]
Abstract
Attenuating the Taxol productivity of fungi with the subculturing and storage under axenic conditions is the challenge that halts the feasibility of fungi to be an industrial platform for Taxol production. This successive weakening of Taxol productivity by fungi could be attributed to the epigenetic down-regulation and molecular silencing of most of the gene clusters encoding Taxol biosynthetic enzymes. Thus, exploring the epigenetic regulating mechanisms controlling the molecular machinery of Taxol biosynthesis could be an alternative prospective technology to conquer the lower accessibility of Taxol by the potent fungi. The current review focuses on discussing the different molecular approaches, epigenetic regulators, transcriptional factors, metabolic manipulators, microbial communications and microbial cross-talking approaches on restoring and enhancing the Taxol biosynthetic potency of fungi to be industrial platform for Taxol production.
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Affiliation(s)
- Nabil Z Mohamed
- Enzymology and Fungal Biotechnology Lab, Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt
| | - Lamis Shaban
- Enzymology and Fungal Biotechnology Lab, Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt.
| | - Samia Safan
- Enzymology and Fungal Biotechnology Lab, Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt
| | - Ashraf S A El-Sayed
- Enzymology and Fungal Biotechnology Lab, Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt.
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5
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Kun RS, Salazar-Cerezo S, Peng M, Zhang Y, Savage E, Lipzen A, Ng V, Grigoriev IV, de Vries RP, Garrigues S. The Amylolytic Regulator AmyR of Aspergillus niger Is Involved in Sucrose and Inulin Utilization in a Culture-Condition-Dependent Manner. J Fungi (Basel) 2023; 9:jof9040438. [PMID: 37108893 PMCID: PMC10142829 DOI: 10.3390/jof9040438] [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: 02/17/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
Filamentous fungi degrade complex plant material to its monomeric building blocks, which have many biotechnological applications. Transcription factors play a key role in plant biomass degradation, but little is known about their interactions in the regulation of polysaccharide degradation. Here, we deepened the knowledge about the storage polysaccharide regulators AmyR and InuR in Aspergillus niger. AmyR controls starch degradation, while InuR is involved in sucrose and inulin utilization. In our study, the phenotypes of A. niger parental, ΔamyR, ΔinuR and ΔamyRΔinuR strains were assessed in both solid and liquid media containing sucrose or inulin as carbon source to evaluate the roles of AmyR and InuR and the effect of culture conditions on their functions. In correlation with previous studies, our data showed that AmyR has a minor contribution to sucrose and inulin utilization when InuR is active. In contrast, growth profiles and transcriptomic data showed that the deletion of amyR in the ΔinuR background strain resulted in more pronounced growth reduction on both substrates, mainly evidenced by data originating from solid cultures. Overall, our results show that submerged cultures do not always reflect the role of transcription factors in the natural growth condition, which is better represented on solid substrates. Importance: The type of growth has critical implications in enzyme production by filamentous fungi, a process that is controlled by transcription factors. Submerged cultures are the preferred setups in laboratory and industry and are often used for studying the physiology of fungi. In this study, we showed that the genetic response of A. niger to starch and inulin was highly affected by the culture condition, since the transcriptomic response obtained in a liquid environment did not fully match the behavior of the fungus in a solid environment. These results have direct implications in enzyme production and would help industry choose the best approaches to produce specific CAZymes for industrial purposes.
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Affiliation(s)
- Roland S Kun
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Sonia Salazar-Cerezo
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Yu Zhang
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Emily Savage
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Anna Lipzen
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Vivian Ng
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Igor V Grigoriev
- USA Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Sandra Garrigues
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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6
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Mattam AJ, Chaudhari YB, Velankar HR. Factors regulating cellulolytic gene expression in filamentous fungi: an overview. Microb Cell Fact 2022; 21:44. [PMID: 35317826 PMCID: PMC8939176 DOI: 10.1186/s12934-022-01764-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 02/27/2022] [Indexed: 12/19/2022] Open
Abstract
The growing demand for biofuels such as bioethanol has led to the need for identifying alternative feedstock instead of conventional substrates like molasses, etc. Lignocellulosic biomass is a relatively inexpensive feedstock that is available in abundance, however, its conversion to bioethanol involves a multistep process with different unit operations such as size reduction, pretreatment, saccharification, fermentation, distillation, etc. The saccharification or enzymatic hydrolysis of cellulose to glucose involves a complex family of enzymes called cellulases that are usually fungal in origin. Cellulose hydrolysis requires the synergistic action of several classes of enzymes, and achieving the optimum secretion of these simultaneously remains a challenge. The expression of fungal cellulases is controlled by an intricate network of transcription factors and sugar transporters. Several genetic engineering efforts have been undertaken to modulate the expression of cellulolytic genes, as well as their regulators. This review, therefore, focuses on the molecular mechanism of action of these transcription factors and their effect on the expression of cellulases and hemicellulases.
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Affiliation(s)
- Anu Jose Mattam
- Hindustan Petroleum Green R and D Centre (HPGRDC), KIADB Industrial Area, Tarabanahalli, Devanagundi, Hoskote, Bangalore, 560067, India
| | - Yogesh Babasaheb Chaudhari
- Hindustan Petroleum Green R and D Centre (HPGRDC), KIADB Industrial Area, Tarabanahalli, Devanagundi, Hoskote, Bangalore, 560067, India
| | - Harshad Ravindra Velankar
- Hindustan Petroleum Green R and D Centre (HPGRDC), KIADB Industrial Area, Tarabanahalli, Devanagundi, Hoskote, Bangalore, 560067, India.
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7
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Lengyel S, Rascle C, Poussereau N, Bruel C, Sella L, Choquer M, Favaron F. Snf1 Kinase Differentially Regulates Botrytis cinerea Pathogenicity according to the Plant Host. Microorganisms 2022; 10:microorganisms10020444. [PMID: 35208900 PMCID: PMC8877277 DOI: 10.3390/microorganisms10020444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/04/2022] [Accepted: 02/11/2022] [Indexed: 11/16/2022] Open
Abstract
The Snf1 kinase of the glucose signaling pathway controls the response to nutritional and environmental stresses. In phytopathogenic fungi, Snf1 acts as a global activator of plant cell wall degrading enzymes that are major virulence factors for plant colonization. To characterize its role in the virulence of the necrotrophic fungus Botrytis cinerea, two independent deletion mutants of the Bcsnf1 gene were obtained and analyzed. Virulence of the Δsnf1 mutants was reduced by 59% on a host with acidic pH (apple fruit) and up to 89% on hosts with neutral pH (cucumber cotyledon and French bean leaf). In vitro, Δsnf1 mutants grew slower than the wild type strain at both pH 5 and 7, with a reduction of 20–80% in simple sugars, polysaccharides, and lipidic carbon sources, and these defects were amplified at pH 7. A two-fold reduction in secretion of xylanase activities was observed consequently to the Bcsnf1 gene deletion. Moreover, Δsnf1 mutants were altered in their ability to control ambient pH. Finally, Δsnf1 mutants were impaired in asexual sporulation and did not produce macroconidia. These results confirm the importance of BcSnf1 in pathogenicity, nutrition, and conidiation, and suggest a role in pH regulation for this global regulator in filamentous fungi.
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Affiliation(s)
- Szabina Lengyel
- Department of Land, Environment, Agriculture and Forestry (TESAF), University of Padova, Viale dell’Università, 16, 35020 Legnaro, Italy; (S.L.); (F.F.)
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Bayer SAS, INSA Lyon, UMR5240, Microbiologie, Adaptation et Pathogénie, 14 Impasse Pierre Baizet, F-69263 Lyon, France; (C.R.); (N.P.); (C.B.)
| | - Christine Rascle
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Bayer SAS, INSA Lyon, UMR5240, Microbiologie, Adaptation et Pathogénie, 14 Impasse Pierre Baizet, F-69263 Lyon, France; (C.R.); (N.P.); (C.B.)
| | - Nathalie Poussereau
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Bayer SAS, INSA Lyon, UMR5240, Microbiologie, Adaptation et Pathogénie, 14 Impasse Pierre Baizet, F-69263 Lyon, France; (C.R.); (N.P.); (C.B.)
| | - Christophe Bruel
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Bayer SAS, INSA Lyon, UMR5240, Microbiologie, Adaptation et Pathogénie, 14 Impasse Pierre Baizet, F-69263 Lyon, France; (C.R.); (N.P.); (C.B.)
| | - Luca Sella
- Department of Land, Environment, Agriculture and Forestry (TESAF), University of Padova, Viale dell’Università, 16, 35020 Legnaro, Italy; (S.L.); (F.F.)
- Correspondence: (L.S.); (M.C.)
| | - Mathias Choquer
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Bayer SAS, INSA Lyon, UMR5240, Microbiologie, Adaptation et Pathogénie, 14 Impasse Pierre Baizet, F-69263 Lyon, France; (C.R.); (N.P.); (C.B.)
- Correspondence: (L.S.); (M.C.)
| | - Francesco Favaron
- Department of Land, Environment, Agriculture and Forestry (TESAF), University of Padova, Viale dell’Università, 16, 35020 Legnaro, Italy; (S.L.); (F.F.)
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8
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Chroumpi T, Martínez-Reyes N, Kun RS, Peng M, Lipzen A, Ng V, Tejomurthula S, Zhang Y, Grigoriev IV, Mäkelä MR, de Vries RP, Garrigues S. Detailed analysis of the D-galactose catabolic pathways in Aspergillus niger reveals complexity at both metabolic and regulatory level. Fungal Genet Biol 2022; 159:103670. [PMID: 35121171 DOI: 10.1016/j.fgb.2022.103670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 12/22/2021] [Accepted: 01/28/2022] [Indexed: 01/23/2023]
Abstract
The current impetus towards a sustainable bio-based economy has accelerated research to better understand the mechanisms through which filamentous fungi convert plant biomass, a valuable feedstock for biotechnological applications. Several transcription factors have been reported to control the polysaccharide degradation and metabolism of the resulting sugars in fungi. However, little is known about their individual contributions, interactions and crosstalk. D-galactose is a hexose sugar present mainly in hemicellulose and pectin in plant biomass. Here, we study D-galactose conversion by Aspergillus niger and describe the involvement of the arabinanolytic and xylanolytic activators AraR and XlnR, in addition to the D-galactose-responsive regulator GalX. Our results deepen the understanding of the complexity of the filamentous fungal regulatory network for plant biomass degradation and sugar catabolism, and facilitate the generation of more efficient plant biomass-degrading strains for biotechnological applications.
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Affiliation(s)
- Tania Chroumpi
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Natalia Martínez-Reyes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Roland S Kun
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Vivian Ng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Sravanthi Tejomurthula
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Yu Zhang
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, United States
| | - Miia R Mäkelä
- Department of Microbiology, P.O. Box 56, Viikinkaari 9, University of Helsinki, Helsinki, Finland
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Sandra Garrigues
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
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9
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Gan Y, Qi X, Lin Y, Guo Y, Zhang Y, Wang Q. A Hierarchical Transcriptional Regulatory Network Required for Long-Term Thermal Stress Tolerance in an Industrial Saccharomyces cerevisiae Strain. Front Bioeng Biotechnol 2022; 9:826238. [PMID: 35118059 PMCID: PMC8804346 DOI: 10.3389/fbioe.2021.826238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 12/30/2021] [Indexed: 11/13/2022] Open
Abstract
Yeast cells suffer from continuous and long-term thermal stress during high-temperature ethanol fermentation. Understanding the mechanism of yeast thermotolerance is important not only for studying microbial stress biology in basic research but also for developing thermotolerant strains for industrial application. Here, we compared the effects of 23 transcription factor (TF) deletions on high-temperature ethanol fermentation and cell survival after heat shock treatment and identified three core TFs, Sin3p, Srb2p and Mig1p, that are involved in regulating the response to long-term thermotolerance. Further analyses of comparative transcriptome profiling of the core TF deletions and transcription regulatory associations revealed a hierarchical transcriptional regulatory network centered on these three TFs. This global transcriptional regulatory network provided a better understanding of the regulatory mechanism behind long-term thermal stress tolerance as well as potential targets for transcriptome engineering to improve the performance of high-temperature ethanol fermentation by an industrial Saccharomyces cerevisiae strain.
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Affiliation(s)
- Yuman Gan
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Xianni Qi
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Yuping Lin
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
- *Correspondence: Qinhong Wang, ; Yuping Lin,
| | - Yufeng Guo
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Yuanyuan Zhang
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Qinhong Wang
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
- *Correspondence: Qinhong Wang, ; Yuping Lin,
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10
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Li T, Su X, Qu H, Duan X, Jiang Y. Biosynthesis, regulation, and biological significance of fumonisins in fungi: current status and prospects. Crit Rev Microbiol 2021; 48:450-462. [PMID: 34550845 DOI: 10.1080/1040841x.2021.1979465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Fumonisins are one of the most important mycotoxin classes due to their widespread occurrence and potential health threat to humans and animals. Currently, most of the research focuses on the control of fumonisin contamination in the food supply chain. In recent years, significant progress in biochemistry, enzymology, and genetic regulation of fumonisin biosynthesis has been achieved using molecular technology. Furthermore, new insights into the roles of fumonisins in the interaction between fungi and plant hosts have been reported. This review provides an overview of the current understanding of the biosynthesis and regulation of fumonisins. The ecological significance of fumonisins to Fusarium species that produce the toxins is discussed, and the complex regulatory networks of fumonisin synthesis is proposed.
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Affiliation(s)
- Taotao Li
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xinguo Su
- Tropical Agriculture and Forestry Department, Guangdong AIB Polytechnic College, Guangzhou, China
| | - Hongxia Qu
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xuewu Duan
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Yueming Jiang
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,College of Life Sciences, Gannan Normal University, Ganzhou, China
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11
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Gabriel R, Mueller R, Floerl L, Hopson C, Harth S, Schuerg T, Fleissner A, Singer SW. CAZymes from the thermophilic fungus Thermoascus aurantiacus are induced by C5 and C6 sugars. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:169. [PMID: 34384463 PMCID: PMC8359064 DOI: 10.1186/s13068-021-02018-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Filamentous fungi are excellent lignocellulose degraders, which they achieve through producing carbohydrate active enzymes (CAZymes). CAZyme production is highly orchestrated and gene expression analysis has greatly expanded understanding of this important biotechnological process. The thermophilic fungus Thermoascus aurantiacus secretes highly active thermostable enzymes that enable saccharifications at higher temperatures; however, the genome-wide measurements of gene expression in response to CAZyme induction are not understood. RESULTS A fed-batch system with plant biomass-derived sugars D-xylose, L-arabinose and cellobiose established that these sugars induce CAZyme expression in T. aurantiacus. The C5 sugars induced both cellulases and hemicellulases, while cellobiose specifically induced cellulases. A minimal medium formulation was developed to enable gene expression studies of T. aurantiacus with these inducers. It was found that d-xylose and L-arabinose strongly induced a wide variety of CAZymes, auxiliary activity (AA) enzymes and carbohydrate esterases (CEs), while cellobiose facilitated lower expression of mostly cellulase genes. Furthermore, putative orthologues of different unfolded protein response genes were up-regulated during the C5 sugar feeding together with genes in the C5 sugar assimilation pathways. CONCLUSION This work has identified two additional CAZyme inducers for T. aurantiacus, L-arabinose and cellobiose, along with D-xylose. A combination of biochemical assays and RNA-seq measurements established that C5 sugars induce a suite of cellulases and hemicellulases, providing paths to produce broad spectrum thermotolerant enzymatic mixtures.
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Affiliation(s)
- Raphael Gabriel
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Institut Für Genetik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Rebecca Mueller
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Institut Für Genetik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Lena Floerl
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190, Vienna, Austria
- Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Cynthia Hopson
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Department of Chemical Engineering and Materials, Faculty of Chemistry, Complutense University of Madrid, Av. Complutense s/n, 28040, Madrid, Spain
| | - Simon Harth
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Frankfurt Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Timo Schuerg
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
| | - Andre Fleissner
- Institut Für Genetik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Rebenring 56, 38106, Braunschweig, Germany
| | - Steven W Singer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA.
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.
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12
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The F-box protein gene exo- 1 is a target for reverse engineering enzyme hypersecretion in filamentous fungi. Proc Natl Acad Sci U S A 2021; 118:2025689118. [PMID: 34168079 DOI: 10.1073/pnas.2025689118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Carbohydrate active enzymes (CAZymes) are vital for the lignocellulose-based biorefinery. The development of hypersecreting fungal protein production hosts is therefore a major aim for both academia and industry. However, despite advances in our understanding of their regulation, the number of promising candidate genes for targeted strain engineering remains limited. Here, we resequenced the genome of the classical hypersecreting Neurospora crassa mutant exo-1 and identified the causative point of mutation to reside in the F-box protein-encoding gene, NCU09899. The corresponding deletion strain displayed amylase and invertase activities exceeding those of the carbon catabolite derepressed strain Δcre-1, while glucose repression was still mostly functional in Δexo-1 Surprisingly, RNA sequencing revealed that while plant cell wall degradation genes are broadly misexpressed in Δexo-1, only a small fraction of CAZyme genes and sugar transporters are up-regulated, indicating that EXO-1 affects specific regulatory factors. Aiming to elucidate the underlying mechanism of enzyme hypersecretion, we found the high secretion of amylases and invertase in Δexo-1 to be completely dependent on the transcriptional regulator COL-26. Furthermore, misregulation of COL-26, CRE-1, and cellular carbon and nitrogen metabolism was confirmed by proteomics. Finally, we successfully transferred the hypersecretion trait of the exo-1 disruption by reverse engineering into the industrially deployed fungus Myceliophthora thermophila using CRISPR-Cas9. Our identification of an important F-box protein demonstrates the strength of classical mutants combined with next-generation sequencing to uncover unanticipated candidates for engineering. These data contribute to a more complete understanding of CAZyme regulation and will facilitate targeted engineering of hypersecretion in further organisms of interest.
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13
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Pirayre A, Duval L, Blugeon C, Firmo C, Perrin S, Jourdier E, Margeot A, Bidard F. Glucose-lactose mixture feeds in industry-like conditions: a gene regulatory network analysis on the hyperproducing Trichoderma reesei strain Rut-C30. BMC Genomics 2020; 21:885. [PMID: 33302864 PMCID: PMC7731781 DOI: 10.1186/s12864-020-07281-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/25/2020] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The degradation of cellulose and hemicellulose molecules into simpler sugars such as glucose is part of the second generation biofuel production process. Hydrolysis of lignocellulosic substrates is usually performed by enzymes produced and secreted by the fungus Trichoderma reesei. Studies identifying transcription factors involved in the regulation of cellulase production have been conducted but no overview of the whole regulation network is available. A transcriptomic approach with mixtures of glucose and lactose, used as a substrate for cellulase induction, was used to help us decipher missing parts in the network of T. reesei Rut-C30. RESULTS Experimental results on the Rut-C30 hyperproducing strain confirmed the impact of sugar mixtures on the enzymatic cocktail composition. The transcriptomic study shows a temporal regulation of the main transcription factors and a lactose concentration impact on the transcriptional profile. A gene regulatory network built using BRANE Cut software reveals three sub-networks related to i) a positive correlation between lactose concentration and cellulase production, ii) a particular dependence of the lactose onto the β-glucosidase regulation and iii) a negative regulation of the development process and growth. CONCLUSIONS This work is the first investigating a transcriptomic study regarding the effects of pure and mixed carbon sources in a fed-batch mode. Our study expose a co-orchestration of xyr1, clr2 and ace3 for cellulase and hemicellulase induction and production, a fine regulation of the β-glucosidase and a decrease of growth in favor of cellulase production. These conclusions provide us with potential targets for further genetic engineering leading to better cellulase-producing strains in industry-like conditions.
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Affiliation(s)
- Aurélie Pirayre
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, Rueil-Malmaison, 92852, France.
| | - Laurent Duval
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, Rueil-Malmaison, 92852, France
- Laboratoire d'Informatique Gaspard-Monge (LIGM), ESIEE Paris, Université-Gustave Eiffel, Marne-la-Vallée, F-77454, France
| | - Corinne Blugeon
- Genomic facility, Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Cyril Firmo
- Genomic facility, Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Sandrine Perrin
- Genomic facility, Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Etienne Jourdier
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, Rueil-Malmaison, 92852, France
| | - Antoine Margeot
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, Rueil-Malmaison, 92852, France
| | - Frédérique Bidard
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, Rueil-Malmaison, 92852, France
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Asemoloye MD, Tosi S, Daccò C, Wang X, Xu S, Marchisio MA, Gao W, Jonathan SG, Pecoraro L. Hydrocarbon Degradation and Enzyme Activities of Aspergillus oryzae and Mucor irregularis Isolated from Nigerian Crude Oil-Polluted Sites. Microorganisms 2020; 8:E1912. [PMID: 33266344 PMCID: PMC7761101 DOI: 10.3390/microorganisms8121912] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/26/2020] [Accepted: 11/28/2020] [Indexed: 12/23/2022] Open
Abstract
Many free-living saprobic fungi are nature recruited organisms for the degradation of wastes, ranging from lignocellulose biomass to organic/inorganic chemicals, aided by their production of enzymes. In this study, fungal strains were isolated from contaminated crude-oil fields in Nigeria. The dominant fungi were selected from each site and identified as Aspergillus oryzae and Mucor irregularis based on morphological and molecular characterization, with site percentage incidences of 56.67% and 66.70%, respectively. Selected strains response/tolerance to complex hydrocarbon (used engine oil) was studied by growing them on Bushnell Haas (BH) mineral agar supplemented with the hydrocarbon at different concentrations, i.e., 5%, 10%, 15%, and 20%, with a control having dextrose. Hydrocarbon degradation potentials of these fungi were confirmed in BH broth culture filtrates pre-supplemented with 1% engine oil after 15 days of incubation using GC/MS. In addition, the presence of putative enzymes, laccase (Lac), manganese peroxidase (MnP), and lignin peroxidase (LiP) was confirmed in culture filtrates using appropriate substrates. The analyzed fungi grew in hydrocarbon supplemented medium with no other carbon source and exhibited 39.40% and 45.85% dose inhibition response (DIR) respectively at 20% hydrocarbon concentration. An enzyme activity test revealed that these two fungi produced more Lac than MnP and LiP. It was also observed through the GC/MS analyses that while A. oryzae acted on all hydrocarbon components in the used engine oil, M. irregularis only degraded the long-chain hydrocarbons and BTEX. This study confirms that A. oryzae and M. irregularis have the potential to be exploited in the bio-treatment and removal of hydrocarbons from polluted soils.
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Affiliation(s)
- Michael Dare Asemoloye
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China; (M.D.A.); (X.W.); (S.X.); (W.G.)
| | - Solveig Tosi
- Laboratory of Mycology, Department of Earth and Environmental Sciences, University of Pavia, Via S. Epifanio 14, 27100 Pavia, Italy; (S.T.); (C.D.)
| | - Chiara Daccò
- Laboratory of Mycology, Department of Earth and Environmental Sciences, University of Pavia, Via S. Epifanio 14, 27100 Pavia, Italy; (S.T.); (C.D.)
| | - Xiao Wang
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China; (M.D.A.); (X.W.); (S.X.); (W.G.)
| | - Shihan Xu
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China; (M.D.A.); (X.W.); (S.X.); (W.G.)
| | - Mario Andrea Marchisio
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China; (M.D.A.); (X.W.); (S.X.); (W.G.)
| | - Wenyuan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China; (M.D.A.); (X.W.); (S.X.); (W.G.)
| | - Segun Gbolagade Jonathan
- Mycology & Applied Microbiology Group, Department of Botany, University of Ibadan, Ibadan 200284, Oyo State, Nigeria;
| | - Lorenzo Pecoraro
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China; (M.D.A.); (X.W.); (S.X.); (W.G.)
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15
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Li J, Chen G, Zhang J, Shen H, Kang J, Feng P, Xie Q, Hu Z. Suppression of a hexokinase gene, SlHXK1, leads to accelerated leaf senescence and stunted plant growth in tomato. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 298:110544. [PMID: 32771157 DOI: 10.1016/j.plantsci.2020.110544] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 05/19/2020] [Accepted: 05/27/2020] [Indexed: 05/18/2023]
Abstract
Sugars are the key regulatory molecules that impact diverse biological processes in plants. Hexokinase, the key rate-limiting enzyme in hexose metabolism, takes part in the first step of glycolytic pathway. Acting as a sensor that mediates sugar regulation, hexokinase has been proved to play significant roles in regulating plant growth and development. Here, we isolated a hexokinase gene SlHXK1 from tomato. Its transcript levels were higher in flowers and leaves than in other organs and decreased during leaf and petiole development. SlHXK1-RNAi lines displayed advanced leaf senescence and stunted plant growth. Physiological features including plant height, leaf length, thickness and size, the contents of chlorophyll, starch and MDA, and hexokinase activity were dramatically altered in SlHXK1-RNAi plants. Dark-induced leaf senescence were advanced and the transcripts of senescence-related genes after darkness treatment were markedly increased in SlHXK1-RNAi plants. RNA-seq and qRT-PCR analyses showed that the transcripts of genes related to plant hormones, photosynthesis, chloroplast development, chlorophyll synthesis and metabolism, cellular process, starch and sucrose metabolism, and senescence were significantly altered in SlHXK1-RNAi plants. Taken together, our data demonstrate that SlHXK1 is a significant gene involved in leaf senescence and plant growth and development in tomato through affecting starch turnover.
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Affiliation(s)
- Jing Li
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Guoping Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Jianling Zhang
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Hui Shen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Jing Kang
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Panpan Feng
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Qiaoli Xie
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
| | - Zongli Hu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.
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16
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Transcriptional regulatory proteins in central carbon metabolism of Pichia pastoris and Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2020; 104:7273-7311. [PMID: 32651601 DOI: 10.1007/s00253-020-10680-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 05/04/2020] [Accepted: 05/10/2020] [Indexed: 01/21/2023]
Abstract
System-wide interactions in living cells and discovery of the diverse roles of transcriptional regulatory proteins that are mediator proteins with catalytic domains and regulatory subunits and transcription factors in the cellular pathways have become crucial for understanding the cellular response to environmental conditions. This review provides information for future metabolic engineering strategies through analyses on the highly interconnected regulatory networks in Saccharomyces cerevisiae and Pichia pastoris and identifying their components. We discuss the current knowledge on the carbon catabolite repression (CCR) mechanism, interconnecting regulatory system of the central metabolic pathways that regulate cell metabolism based on nutrient availability in the industrial yeasts. The regulatory proteins and their functions in the CCR signalling pathways in both yeasts are presented and discussed. We highlight the importance of metabolic signalling networks by signifying ways on how effective engineering strategies can be designed for generating novel regulatory circuits, furthermore to activate pathways that reconfigure the network architecture. We summarize the evidence that engineering of multilayer regulation is needed for directed evolution of the cellular network by putting the transcriptional control into a new perspective for the regulation of central carbon metabolism of the industrial yeasts; furthermore, we suggest research directions that may help to enhance production of recombinant products in the widely used, creatively engineered, but relatively less studied P. pastoris through de novo metabolic engineering strategies based on the discovery of components of signalling pathways in CCR metabolism. KEY POINTS: • Transcriptional regulation and control is the key phenomenon in the cellular processes. • Designing de novo metabolic engineering strategies depends on the discovery of signalling pathways in CCR metabolism. • Crosstalk between pathways occurs through essential parts of transcriptional machinery connected to specific catalytic domains. • In S. cerevisiae, a major part of CCR metabolism is controlled through Snf1 kinase, Glc7 phosphatase, and Srb10 kinase. • In P. pastoris, signalling pathways in CCR metabolism have not yet been clearly known yet. • Cellular regulations on the transcription of promoters are controlled with carbon sources.
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17
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Durán-Aranguren D, Chiriví-Salomón J, Anaya L, Durán-Sequeda D, Cruz L, Serrano J, Sarmiento L, Restrepo S, Sanjuan T, Sierra R. Effect of bioactive compounds extracted from Cordyceps nidus ANDES-F1080 on laccase activity of Pleurotus ostreatus ANDES-F515. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2020; 26:e00466. [PMID: 32617265 PMCID: PMC7322798 DOI: 10.1016/j.btre.2020.e00466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 04/21/2020] [Accepted: 05/04/2020] [Indexed: 06/11/2023]
Abstract
Laccases are ligninolytic enzymes produced by different microorganisms, especially by fungi such as the white-rot fungus Pleurotus ostreatus. Chemical inductors have been used to promote laccase secretion due to the application of these enzymes in lignocellulosic biomass pretreatment. Cordyceps nidus ANDES-F1080 was previously described as a source of bioactive compounds that could influence the enzymatic production system of other fungi. For that reason, this study evaluates the effect of C. nidus' ANDES-F1080 extracts on the laccase activity of P. ostreatus ANDES-F515. To achieve this objective, C. nidus ANDES-F1080 was grown in four different substrates: two artificial-based and two natural-based culture media. Metabolites were extracted from C. nidus ANDES-F1080 using water and methanol as solvents. Biochemical characterization of these extracts was performed to complement the analysis of their effect on laccase activity. Our results revealed an enhancement on the laccase activity of P. ostreatus ANDES-F515 grown in natural-based cultures when C. nidus' ANDES-F1080 extracts were supplemented. The best laccase activities registered values around 10,575 ± 813 U·L-1.
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Affiliation(s)
- D. Durán-Aranguren
- Product and Processes Design Group, Department of Chemical Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - J.S. Chiriví-Salomón
- Product and Processes Design Group, Department of Chemical Engineering, Universidad de Los Andes, Bogotá, Colombia
- Conservación, Bioprospección y Desarrollo Sostenible, Escuela de Ciencias Agrícolas, Pecuarias y del Medio Ambiente, Universidad Nacional Abierta y a Distancia, Bogotá, Colombia
| | - L. Anaya
- Product and Processes Design Group, Department of Chemical Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - D. Durán-Sequeda
- Product and Processes Design Group, Department of Chemical Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - L.J. Cruz
- Product and Processes Design Group, Department of Chemical Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - J.D. Serrano
- Product and Processes Design Group, Department of Chemical Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - L. Sarmiento
- Product and Processes Design Group, Department of Chemical Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - S. Restrepo
- Laboratory of Mycology and Plant Diseases, Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | - T. Sanjuan
- Product and Processes Design Group, Department of Chemical Engineering, Universidad de Los Andes, Bogotá, Colombia
| | - R. Sierra
- Product and Processes Design Group, Department of Chemical Engineering, Universidad de Los Andes, Bogotá, Colombia
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18
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Kun RS, Meng J, Salazar-Cerezo S, Mäkelä MR, de Vries RP, Garrigues S. CRISPR/Cas9 facilitates rapid generation of constitutive forms of transcription factors in Aspergillus niger through specific on-site genomic mutations resulting in increased saccharification of plant biomass. Enzyme Microb Technol 2020; 136:109508. [PMID: 32331715 DOI: 10.1016/j.enzmictec.2020.109508] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/16/2019] [Accepted: 01/08/2020] [Indexed: 12/26/2022]
Abstract
The CRISPR/Cas9 system has been successfully applied for gene editing in filamentous fungi. Previous studies reported that single stranded oligonucleotides can be used as repair templates to induce point mutations in some filamentous fungi belonging to genus Aspergillus. In Aspergillus niger, extensive research has been performed on regulation of plant biomass degradation, addressing transcription factors such as XlnR or GaaR, involved in (hemi-)cellulose and pectin utilization, respectively. Single nucleotide mutations leading to constitutively active forms of XlnR and GaaR have been previously reported. However, the mutations were performed by the introduction of versions obtained through site-directed or UV-mutagenesis into the genome. Here we report a more time- and cost-efficient approach to obtaining constitutively active versions by application of the CRISPR/Cas9 system to generate the desired mutation on-site in the A. niger genome. This was also achieved using only 60-mer single stranded oligonucleotides, shorter than the previously reported 90-mer strands. In this study, we show that CRISPR/Cas9 can also be used to efficiently change functional properties of the proteins encoded by the target gene by on-site genomic mutations in A. niger. The obtained strains with constitutively active XlnR and GaaR versions resulted in increased production of plant biomass degrading enzymes and improved release of d-xylose and l-arabinose from wheat bran, and d-galacturonic acid from sugar beet pulp.
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Affiliation(s)
- Roland S Kun
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Jiali Meng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Sonia Salazar-Cerezo
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Miia R Mäkelä
- Fungal Genetics and Biotechnology, Department of Microbiology, University of Helsinki, Viikinkaari 9, 00790 Helsinki, Finland
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Sandra Garrigues
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
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Chen Y, Kistler HC, Ma Z. Fusarium graminearum Trichothecene Mycotoxins: Biosynthesis, Regulation, and Management. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:15-39. [PMID: 30893009 DOI: 10.1146/annurev-phyto-082718-100318] [Citation(s) in RCA: 203] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Fusarium head blight (FHB) of small grain cereals caused by Fusarium graminearum and other Fusarium species is an economically important plant disease worldwide. Fusarium infections not only result in severe yield losses but also contaminate grain with various mycotoxins, especially deoxynivalenol (DON). With the complete genome sequencing of F. graminearum, tremendous progress has been made during the past two decades toward understanding the basis for DON biosynthesis and its regulation. Here, we summarize the current understanding of DON biosynthesis and the effect of regulators, signal transduction pathways, and epigenetic modifications on DON production and the expression of biosynthetic TRI genes. In addition, strategies for controlling FHB and DON contamination are reviewed. Further studies on these biosynthetic and regulatory systems will provide useful knowledge for developing novel management strategies to prevent FHB incidence and mycotoxin accumulation in cereals.
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Affiliation(s)
- Yun Chen
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China;
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - H Corby Kistler
- Cereal Disease Laboratory, Agricultural Research Service, United States Department of Agriculture, Saint Paul, Minnesota 55108, USA
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China;
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
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Crosstalk of Cellulose and Mannan Perception Pathways Leads to Inhibition of Cellulase Production in Several Filamentous Fungi. mBio 2019; 10:mBio.00277-19. [PMID: 31266859 PMCID: PMC6606794 DOI: 10.1128/mbio.00277-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In fungi, the production of enzymes for polysaccharide degradation is controlled by complex signaling networks. Previously, these networks were studied in response to simple sugars or single polysaccharides. Here, we tackled for the first time the molecular interplay between two seemingly unrelated perception pathways: those for cellulose and the hemicellulose (gluco)mannan. We identified a so far unknown competitive inhibition between the respective degradation products acting as signaling molecules. Competition was detected both at the level of the uptake and intracellularly, upstream of the main transcriptional regulator CLR-2. Our findings provide novel insights into the molecular communication between perception pathways. Also, they present possible targets for the improvement of industrial strains for higher cellulase production through the engineering of mannan insensitivity. It is essential for microbes to acquire information about their environment. Fungi use soluble degradation products of plant cell wall components to understand the substrate composition they grow on. Individual perception pathways have been well described. However, the interconnections between pathways remain poorly understood. In the present work, we provide evidence of crosstalk between the perception pathways for cellulose and the hemicellulose mannan being conserved in several filamentous fungi and leading to the inhibition of cellulase expression. We used the functional genomics tools available for Neurospora crassa to investigate this overlap at the molecular level. Crosstalk and competitive inhibition could be identified both during uptake by cellodextrin transporters and intracellularly. Importantly, the overlap is independent of CRE-1-mediated catabolite repression. These results provide novel insights into the regulatory networks of lignocellulolytic fungi and will contribute to the rational optimization of fungal enzyme production for efficient plant biomass depolymerization and utilization.
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Shariati S, Zare D, Mirdamadi S. Screening of carbon and nitrogen sources using mixture analysis designs for carotenoid production by Blakeslea trispora. Food Sci Biotechnol 2019; 28:469-479. [PMID: 30956859 DOI: 10.1007/s10068-018-0484-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 08/26/2018] [Accepted: 09/10/2018] [Indexed: 10/28/2022] Open
Abstract
The production of many secondary metabolites such as carotenoids is influenced by the type of carbon and nitrogen sources and C:N ratio applied in culture medium. The present study discusses the role of C:N ratio and screening of carbon and nitrogen sources using mixture analysis design in carotenoids production by Blakeslea trispora. The C:N ratios of 20, 40, and 60 with six nitrogen sources were evaluated. Results indicated that limitation of nitrogen source (C:N of 60) could improve carotenoids production. Six nitrogen and carbon sources were then screened using mixture analysis design. The most effective nitrogen and carbon sources were soybean powder and glucose, respectively. The productivity of carotenoids (983.8 ± 31.5 mg/L) based on consumed nitrogen and carbon source was 189.10 mg/g soybean powder and 19.66 mg/g glucose. Mixture analysis design indicated single carbon and nitrogen source were more effective than a mixture of sources for carotenoids production.
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Affiliation(s)
- Sepideh Shariati
- 1Pharmaceutical Sciences Branch, Islamic Azad University, 1941933111 Tehran, Islamic Republic of Iran
| | - Davood Zare
- 2Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), P. O. Box 33535111, Tehran, Islamic Republic of Iran
| | - Saeed Mirdamadi
- 2Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), P. O. Box 33535111, Tehran, Islamic Republic of Iran
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Lehenberger M, Biedermann PH, Benz JP. Molecular identification and enzymatic profiling of Trypodendron (Curculionidae: Xyloterini) ambrosia beetle-associated fungi of the genus Phialophoropsis (Microascales: Ceratocystidaceae). FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2018.07.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Duan SF, Shi JY, Yin Q, Zhang RP, Han PJ, Wang QM, Bai FY. Reverse Evolution of a Classic Gene Network in Yeast Offers a Competitive Advantage. Curr Biol 2019; 29:1126-1136.e5. [PMID: 30905601 DOI: 10.1016/j.cub.2019.02.038] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 01/04/2019] [Accepted: 02/15/2019] [Indexed: 11/26/2022]
Abstract
Glucose repression is a central regulatory system in yeast that ensures the utilization of carbon sources in a highly economical manner. The galactose (GAL) metabolism network is stringently regulated by glucose repression in yeast and has been a classic system for studying gene regulation. We show here that a Saccharomyces cerevisiae (S. cerevisiae) lineage in spontaneously fermented milk has swapped all its structural GAL genes (GAL2 and the GAL7-10-1 cluster) with early diverged versions through introgression. The rewired GAL network has abolished glucose repression and conversed from a strictly inducible to a constitutive system through polygenic changes in the regulatory components of the network, including a thymine (T) to cytosine (C) and a guanine (G) to adenine (A) transition in the upstream repressing sequence (URS) sites of GAL1 and GAL4, respectively, which impair Mig1p-mediated repression, loss of function of the repressor Gal80p through a T146I substitution in the protein, and subsequent futility of GAL3. Furthermore, the milk lineage of S. cerevisiae has achieved galactose-utilization rate elevation and galactose-over-glucose preference switch through the duplication of the introgressed GAL2 and the loss of function of the main glucose transporter genes HXT6 and HXT7. In addition, we demonstrate that GAL2 requires GAL7 or GAL10 for its expression, and Gal2p likely requires Gal1p for its transportation function in the milk lineage of S. cerevisiae. We show a clear case of reverse evolution of a classic gene network for ecological adaptation and provide new insights into the regulatory model of the canonical GAL network.
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Affiliation(s)
- Shou-Fu Duan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Jun-Yan Shi
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Qi Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Ri-Peng Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Pei-Jie Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi-Ming Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China.
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Transcription Factors Controlling Primary and Secondary Metabolism in Filamentous Fungi: The β-Lactam Paradigm. FERMENTATION-BASEL 2018. [DOI: 10.3390/fermentation4020047] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Schneider WDH, Fontana RC, Mendonça S, de Siqueira FG, Dillon AJP, Camassola M. High level production of laccases and peroxidases from the newly isolated white-rot basidiomycete Marasmiellus palmivorus VE111 in a stirred-tank bioreactor in response to different carbon and nitrogen sources. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.03.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Gene dosage effects in yeast support broader roles for the LOG1, HAM1 and DUT1 genes in detoxification of nucleotide analogues. PLoS One 2018; 13:e0196840. [PMID: 29738539 PMCID: PMC5940212 DOI: 10.1371/journal.pone.0196840] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 04/21/2018] [Indexed: 12/22/2022] Open
Abstract
Purine and pyrimidine analogues have important uses in chemotherapies against cancer, and a better understanding of the mechanisms that cause resistance to these drugs is therefore of importance in cancer treatment. In the yeast Saccharomyces cerevisiae, overexpression of the HAM1 gene encoding inosine triphosphate pyrophosphatase confers resistance to both the purine analogue 6-N-hydroxylaminopurine (HAP) and the pyrimidine analogue 5-fluorouracil (5-FU) (Carlsson et al., 2013, PLoS One 8, e52094). To find out more about the mechanisms of resistance to nucleotide analogues, and possible interdependencies between purine and pyrimidine analogue resistance mechanisms, we screened a plasmid library in yeast for genes that confer HAP resistance when overexpressed. We cloned four such genes: ADE4, DUT1, APT2, and ATR1. We further looked for genetic interactions between these genes and genes previously found to confer resistance to 5-FU. We found that HMS1, LOG1 (YJL055W), HAM1, and ATR1 confer resistance to both 5-FU and HAP, whereas ADE4, DUT1 and APT2 are specific for HAP resistance, and CPA1 and CPA2 specific for 5-FU resistance. Possible mechanisms for 5-FU and HAP detoxification are discussed based on the observed genetic interactions. Based on the effect of LOG1 against both 5-FU and HAP toxicity, we propose that the original function of the LOG (LONELY GUY) family of proteins likely was to degrade non-canonical nucleotides, and that their role in cytokinin production is a later development in some organisms.
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Asemoloye MD, Ahmad R, Jonathan SG. Transcriptomic responses of catalase, peroxidase and laccase encoding genes and enzymatic activities of oil spill inhabiting rhizospheric fungal strains. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 235:55-64. [PMID: 29274538 DOI: 10.1016/j.envpol.2017.12.042] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 12/06/2017] [Accepted: 12/10/2017] [Indexed: 06/07/2023]
Abstract
Fungi are well associated with the degradation of hydrocarbons by the production of different enzymes, among which catalases (CBH), laccases (LCC) and peroxidases (LiP and MnP) are of immense importance. In this study, crude oil tolerance and enzyme secretions were demonstrated by rhizospheric fungal strains. Four most abundant strains were isolated from the rhizosphere of grasses growing in aged oil spill sites and identified through morphological characterization and molecular PCR-amplification of 5.8-28S ribosomal rRNA using ITS1 and ITS4 primers. These strains were subjected to crude oil tolerance test at 0-20% concentrations. Presence and transcriptase responses of putative genes lig (1-6), mnp, cbh (1.1, 1.1 and 11), and lcc encoding lignin peroxidase, manganese peroxidase, catalase, and laccase enzymes respectively were also studied in these strains using RT-PCR. In addition, activities of secreted enzymes by each strain were studied in aliquots. The strains were identified as Aspergillus niger asemoA (KY473958), Talaromyces purpurogenus asemoF (KY488463), Trichoderma harzianum asemoJ (KY488466), and Aspergillus flavus asemoM (KY488467) through sequencing and comparing the sequences' data at NCBI BLAST search software. All the isolated strains showed tolerance to crude oil at 20% concentration, but the growth rate reduced with increasing in oil concentrations. All the isolated strains possess the tested genes and lig 1-6 gene was overexpressed in A. niger and T. harzianum while lcc and mnp genes were moderately expressed in all the four strains. Almost 145 U.mL-1 of lignin and manganese peroxidase, 87 U.mL-1 of catalase, and 180 U.mL-1 of laccase enzymes were produced by these strains and it was also observed that these strain mostly produced studied enzymes in response to increasing crude oil concentrations. Considering the robust nature and diverse production of these catalytic enzymes by these strains, they can be exploited for various bioremediation technologies as well as other biotechnological applications.
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Affiliation(s)
- Michael Dare Asemoloye
- Food and Environmental Mycology/Biotechnology Unit, Department of Botany, University of Ibadan, Ibadan, Nigeria; Department of Environmental Sciences, COMSATS Institute of Information Technology, 22060 Abbottabad, Pakistan.
| | - Rafiq Ahmad
- Department of Environmental Sciences, COMSATS Institute of Information Technology, 22060 Abbottabad, Pakistan.
| | - Segun Gbolagade Jonathan
- Food and Environmental Mycology/Biotechnology Unit, Department of Botany, University of Ibadan, Ibadan, Nigeria
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Mascarin G, Kobori N, Jackson M, Dunlap C, Delalibera Í. Nitrogen sources affect productivity, desiccation tolerance and storage stability ofBeauveria bassianablastospores. J Appl Microbiol 2018; 124:810-820. [DOI: 10.1111/jam.13694] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 12/16/2017] [Accepted: 01/04/2018] [Indexed: 11/30/2022]
Affiliation(s)
- G.M. Mascarin
- Embrapa Meio Ambiente; Jaguariúna SP Brazil
- Crop Bioprotection Research Unit; United States Department of Agriculture; Agriculture Research Service, National Center for Agricultural Utilization Research; Peoria IL USA
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura “Luiz de Queiroz”; Universidade de São Paulo (ESALQ-USP); Piracicaba SP Brazil
| | - N.N. Kobori
- Crop Bioprotection Research Unit; United States Department of Agriculture; Agriculture Research Service, National Center for Agricultural Utilization Research; Peoria IL USA
| | - M.A. Jackson
- Crop Bioprotection Research Unit; United States Department of Agriculture; Agriculture Research Service, National Center for Agricultural Utilization Research; Peoria IL USA
| | - C.A. Dunlap
- Crop Bioprotection Research Unit; United States Department of Agriculture; Agriculture Research Service, National Center for Agricultural Utilization Research; Peoria IL USA
| | - Í. Delalibera
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura “Luiz de Queiroz”; Universidade de São Paulo (ESALQ-USP); Piracicaba SP Brazil
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Suhm T, Habernig L, Rzepka M, Kaimal JM, Andréasson C, Büttner S, Ott M. A novel system to monitor mitochondrial translation in yeast. MICROBIAL CELL (GRAZ, AUSTRIA) 2018; 5:158-164. [PMID: 29487862 PMCID: PMC5826703 DOI: 10.15698/mic2018.03.621] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/02/2018] [Indexed: 11/13/2022]
Abstract
The mitochondrial genome is responsible for the production of a handful of polypeptides that are core subunits of the membrane-bound oxidative phosphorylation system. Until now the mechanistic studies of mitochondrial protein synthesis inside cells have been conducted with inhibition of cytoplasmic protein synthesis to reduce the background of nuclear gene expression with the undesired consequence of major disturbances of cellular signaling cascades. Here we have generated a system that allows direct monitoring of mitochondrial translation in unperturbed cells. A recoded gene for superfolder GFP was inserted into the yeast (Saccharomyces cerevisiae) mitochondrial genome and enabled the detection of translation through fluorescence microscopy and flow cytometry in functional mitochondria. This novel tool allows the investigation of the function and regulation of mitochondrial translation during stress signaling, aging and mitochondrial biogenesis.
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Affiliation(s)
- Tamara Suhm
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
| | - Lukas Habernig
- Institute of Molecular Biosciences, University of Graz, A-8010 Graz, Austria
| | - Magdalena Rzepka
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
| | | | - Claes Andréasson
- Department of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, SE-10691 Stockholm, Sweden
| | - Sabrina Büttner
- Institute of Molecular Biosciences, University of Graz, A-8010 Graz, Austria
- Department of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, SE-10691 Stockholm, Sweden
| | - Martin Ott
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
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Yoav S, Salame TM, Feldman D, Levinson D, Ioelovich M, Morag E, Yarden O, Bayer EA, Hadar Y. Effects of cre1 modification in the white-rot fungus Pleurotus ostreatus PC9: altering substrate preference during biological pretreatment. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:212. [PMID: 30065786 PMCID: PMC6062969 DOI: 10.1186/s13068-018-1209-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 07/18/2018] [Indexed: 05/16/2023]
Abstract
BACKGROUND During the process of bioethanol production, cellulose is hydrolyzed into its monomeric soluble units. For efficient hydrolysis, a chemical and/or mechanical pretreatment step is required. Such pretreatment is designed to increase enzymatic digestibility of the cellulose chains inter alia by de-crystallization of the cellulose chains and by removing barriers, such as lignin from the plant cell wall. Biological pretreatment, in which lignin is decomposed or modified by white-rot fungi, has also been considered. One disadvantage in biological pretreatment, however, is the consumption of the cellulose by the fungus. Thus, fungal species that attack lignin with only minimal cellulose loss are advantageous. The secretomes of white-rot fungi contain carbohydrate-active enzymes (CAZymes) including lignin-modifying enzymes. Thus, modification of secretome composition can alter the ratio of lignin/cellulose degradation. RESULTS Pleurotus ostreatus PC9 was genetically modified to either overexpress or eliminate (by gene replacement) the transcriptional regulator CRE1, known to act as a repressor in the process of carbon catabolite repression. The cre1-overexpressing transformant demonstrated lower secreted cellulolytic activity and slightly increased selectivity (based on the chemical composition of pretreated wheat straw), whereas the knockout transformant demonstrated increased cellulolytic activity and significantly reduced residual cellulose, thereby displaying lower selectivity. Pretreatment of wheat straw using the wild-type PC9 resulted in 2.8-fold higher yields of soluble sugar compared to untreated wheat straw. The overexpression transformant showed similar yields (2.6-fold), but the knockout transformant exhibited lower yields (1.2-fold) of soluble sugar. Based on proteomic secretome analysis, production of numerous CAZymes was affected by modification of the expression level of cre1. CONCLUSIONS The gene cre1 functions as a regulator for expression of fungal CAZymes active against plant cell wall lignocelluloses, hence altering the substrate preference of the fungi tested. While the cre1 knockout resulted in a less efficient biological pretreatment, i.e., less saccharification of the treated biomass, the converse manipulation of cre1 (overexpression) failed to improve efficiency. Despite the inverse nature of the two genetic alterations, the expected "mirror image" (i.e., opposite regulatory response) was not observed, indicating that the secretion level of CAZymes, was not exclusively dependent on CRE1 activity.
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Affiliation(s)
- Shahar Yoav
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100 Israel
| | - Tomer M. Salame
- Flow Cytometry Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Daria Feldman
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100 Israel
| | - Dana Levinson
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100 Israel
| | | | - Ely Morag
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100 Israel
| | - Edward A. Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Yitzhak Hadar
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100 Israel
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Ulfstedt M, Hu GZ, Eklund DM, Ronne H. The Ability of a Charophyte Alga Hexokinase to Restore Glucose Signaling and Glucose Repression of Gene Expression in a Glucose-Insensitive Arabidopsis Hexokinase Mutant Depends on Its Catalytic Activity. FRONTIERS IN PLANT SCIENCE 2018; 9:1887. [PMID: 30619433 PMCID: PMC6306471 DOI: 10.3389/fpls.2018.01887] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 12/06/2018] [Indexed: 05/14/2023]
Abstract
Hexokinases is a family of proteins that is found in all eukaryotes. Hexokinases play key roles in the primary carbon metabolism, where they catalyze the phosphorylation of glucose and fructose, but they have also been shown to be involved in glucose signaling in both yeast and plants. We have characterized the Klebsormidium nitens KnHXK1 gene, the only hexokinase-encoding gene in this charophyte alga. The encoded protein, KnHXK1, is a type B plant hexokinase with an N-terminal membrane anchor localizing the protein to the mitochondrial membranes. We found that KnHXK1 expressed in Arabidopsis thaliana can restore the glucose sensing and glucose repression defects of the glucose-insensitive hexokinase mutant gin2-1. Interestingly, both functions require a catalytically active enzyme, since an inactive double mutant was unable to complement gin2-1. These findings differ from previous results on Arabidopsis AtHXK1 and its orthologs in rice, where catalytic and glucose sensing functions could be separated, but are consistent with recent results on the rice cytoplasmic hexokinase OsHXK7. A model with both catalytic and non-catalytic roles for hexokinases in glucose sensing and glucose repression is discussed.
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Affiliation(s)
- Mikael Ulfstedt
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Guo-Zhen Hu
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - D. Magnus Eklund
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Hans Ronne
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- *Correspondence: Hans Ronne,
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Mobbs CV. Glucose-Induced Transcriptional Hysteresis: Role in Obesity, Metabolic Memory, Diabetes, and Aging. Front Endocrinol (Lausanne) 2018; 9:232. [PMID: 29892261 PMCID: PMC5985453 DOI: 10.3389/fendo.2018.00232] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/23/2018] [Indexed: 01/30/2023] Open
Abstract
During differentiation transient, inducers produce permanent changes in gene expression. A similar phenomenon, transcriptional hysteresis, produced by transient or prolonged exposure to glucose, leads to cumulative, persistent, and largely irreversible effects on glucose-regulated gene expression, and may drive key aspects of metabolic memory, obesity, diabetes, and aging, and explain the protective effects of dietary restriction during aging. The most relevant effects of glucose-induced transcriptional hysteresis are the persistent effects of elevated glucose on genes that control glucose metabolism itself. A key observation is that, as with the lac operon, glucose induces genes that promote glycolysis and inhibits gene expression of alternative metabolic pathways including the pentose pathway, beta oxidation, and the TCA cycle. A similar pattern of metabolic gene expression is observed during aging, suggesting that cumulative exposure to glucose during aging produces this metabolic shift. Conversely, dietary restriction, which increases lifespan and delays age-related impairments, produces the opposite metabolic profile, leading to a shift away from glycolysis and toward the use of alternative substrates, including lipid and ketone metabolisms. The effect of glucose on gene expression leads to a positive feedback loop that leads to metastable persistent expression of genes that promote glycolysis and inhibit alternative pathways, a phenomenon first observed in the regulation of the lac operon. On the other hand, this pattern of gene expression can also be inhibited by activation of peroxisome proliferator activating receptor transcription factors that promote beta oxidation and inhibit metabolism of glucose-derived carbon bonds in the TCA cycle. Several pathological consequences may arise from glucose-induced transcriptional hysteresis. First, elevated glucose induces glycolytic genes in pancreatic beta cells, which induces a semi-stable persistent increase in insulin secretion, which could drive obesity and insulin resistance, and also due to glucose toxicity could eventually lead to beta-cell decompensation and diabetes. Diabetic complications persist even after complete normalization of glucose, a phenomenon known as metabolic memory. This too can be explained by persistent bistable expression of glucose-induced glycolytic genes.
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Adnan M, Zheng W, Islam W, Arif M, Abubakar YS, Wang Z, Lu G. Carbon Catabolite Repression in Filamentous Fungi. Int J Mol Sci 2017; 19:ijms19010048. [PMID: 29295552 PMCID: PMC5795998 DOI: 10.3390/ijms19010048] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 12/13/2017] [Accepted: 12/20/2017] [Indexed: 12/18/2022] Open
Abstract
Carbon Catabolite Repression (CCR) has fascinated scientists and researchers around the globe for the past few decades. This important mechanism allows preferential utilization of an energy-efficient and readily available carbon source over relatively less easily accessible carbon sources. This mechanism helps microorganisms to obtain maximum amount of glucose in order to keep pace with their metabolism. Microorganisms assimilate glucose and highly favorable sugars before switching to less-favored sources of carbon such as organic acids and alcohols. In CCR of filamentous fungi, CreA acts as a transcription factor, which is regulated to some extent by ubiquitination. CreD-HulA ubiquitination ligase complex helps in CreA ubiquitination, while CreB-CreC deubiquitination (DUB) complex removes ubiquitin from CreA, which causes its activation. CCR of fungi also involves some very crucial elements such as Hexokinases, cAMP, Protein Kinase (PKA), Ras proteins, G protein-coupled receptor (GPCR), Adenylate cyclase, RcoA and SnfA. Thorough study of molecular mechanism of CCR is important for understanding growth, conidiation, virulence and survival of filamentous fungi. This review is a comprehensive revision of the regulation of CCR in filamentous fungi as well as an updated summary of key regulators, regulation of different CCR-dependent mechanisms and its impact on various physical characteristics of filamentous fungi.
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Affiliation(s)
- Muhammad Adnan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Bio-Pesticides and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Wenhui Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Bio-Pesticides and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Waqar Islam
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Muhammad Arif
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yakubu Saddeeq Abubakar
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Bio-Pesticides and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Bio-Pesticides and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Bio-Pesticides and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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35
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Lameiras F, Ras C, Ten Pierick A, Heijnen JJ, van Gulik WM. Stoichiometry and kinetics of single and mixed substrate uptake in Aspergillus niger. Bioprocess Biosyst Eng 2017; 41:157-170. [PMID: 29052015 PMCID: PMC5773628 DOI: 10.1007/s00449-017-1854-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 10/11/2017] [Indexed: 01/28/2023]
Abstract
In its natural environment, the filamentous fungus Aspergillus niger grows on decaying fruits and plant material, thereby enzymatically degrading the lignocellulosic constituents (lignin, cellulose, hemicellulose, and pectin) into a mixture of mono- and oligosaccharides. To investigate the kinetics and stoichiometry of growth of this fungus on lignocellulosic sugars, we carried out batch cultivations on six representative monosaccharides (glucose, xylose, mannose, rhamnose, arabinose, and galacturonic acid) and a mixture of these. Growth on these substrates was characterized in terms of biomass yields, oxygen/biomass ratios, and specific conversion rates. Interestingly, in combination, some of the carbon sources were consumed simultaneously and some sequentially. With a previously developed protocol, a sequential chemostat cultivation experiment was performed on a feed mixture of the six substrates. We found that the uptake of glucose, xylose, and mannose could be described with a Michaelis–Menten-type kinetics; however, these carbon sources seem to be competing for the same transport systems, while the uptake of arabinose, galacturonic acid, and rhamnose appeared to be repressed by the presence of other substrates.
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Affiliation(s)
- Francisca Lameiras
- Cell Systems Engineering section, Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Cor Ras
- Cell Systems Engineering section, Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Angela Ten Pierick
- Cell Systems Engineering section, Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Joseph J Heijnen
- Cell Systems Engineering section, Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Walter M van Gulik
- Cell Systems Engineering section, Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, The Netherlands.
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36
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Kumar D, Barad S, Chen Y, Luo X, Tannous J, Dubey A, Glam Matana N, Tian S, Li B, Keller N, Prusky D. LaeA regulation of secondary metabolism modulates virulence in Penicillium expansum and is mediated by sucrose. MOLECULAR PLANT PATHOLOGY 2017; 18:1150-1163. [PMID: 27528575 PMCID: PMC6638289 DOI: 10.1111/mpp.12469] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/10/2016] [Accepted: 08/11/2016] [Indexed: 05/11/2023]
Abstract
Penicillium expansum, the causal agent of blue mould rot, is a critical health concern because of the production of the mycotoxin patulin in colonized apple fruit tissue. Although patulin is produced by many Penicillium species, the factor(s) activating its biosynthesis are not clear. Sucrose, a key sugar component of apple fruit, was found to modulate patulin accumulation in a dose-responsive pattern. An increase in sucrose culture amendment from 15 to 175 mm decreased both patulin accumulation and expression of the global regulator laeA by 175- and five-fold, respectively, whilst increasing expression of the carbon catabolite repressor creA. LaeA was found to regulate several secondary metabolite genes, including the patulin gene cluster and concomitant patulin synthesis in vitro. Virulence studies of ΔlaeA mutants of two geographically distant P. expansum isolates (Pe-21 from Israel and Pe-T01 from China) showed differential reduction in disease severity in freshly harvested fruit, ranging from no reduction for Ch-Pe-T01 strains to 15%-25% reduction for both strains in mature fruit, with the ΔlaeA strains of Is-Pe-21 always showing a greater loss in virulence. The results suggest the importance of abiotic factors in LaeA regulation of patulin and other secondary metabolites that contribute to pathogenicity.
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Affiliation(s)
- Dilip Kumar
- Department of Postharvest Science of Fresh ProduceAgricultural Research Organization, The Volcani CenterBet Dagan50250Israel
| | - Shiri Barad
- Department of Postharvest Science of Fresh ProduceAgricultural Research Organization, The Volcani CenterBet Dagan50250Israel
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovot76100Israel
| | - Yong Chen
- Key Laboratory of Plant ResourcesInstitute of Botany, Chinese Academy of SciencesBeijing100093China
| | - Xingyu Luo
- Department of Plant PathologyUniversity of Wisconsin – MadisonMadisonWI53706‐1598USA
| | - Joanna Tannous
- Department of Medical Microbiology and ImmunologyUniversity of Wisconsin – MadisonMadisonWI53706‐1598USA
| | - Amit Dubey
- Department of Postharvest Science of Fresh ProduceAgricultural Research Organization, The Volcani CenterBet Dagan50250Israel
| | - Nofar Glam Matana
- Department of Postharvest Science of Fresh ProduceAgricultural Research Organization, The Volcani CenterBet Dagan50250Israel
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovot76100Israel
| | - Shiping Tian
- Key Laboratory of Plant ResourcesInstitute of Botany, Chinese Academy of SciencesBeijing100093China
| | - Boqiang Li
- Key Laboratory of Plant ResourcesInstitute of Botany, Chinese Academy of SciencesBeijing100093China
| | - Nancy Keller
- Department of Plant PathologyUniversity of Wisconsin – MadisonMadisonWI53706‐1598USA
- Department of Medical Microbiology and ImmunologyUniversity of Wisconsin – MadisonMadisonWI53706‐1598USA
- Department of BacteriologyUniversity of Wisconsin – MadisonMadisonWI53706‐1598USA
| | - Dov Prusky
- Department of Postharvest Science of Fresh ProduceAgricultural Research Organization, The Volcani CenterBet Dagan50250Israel
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Kuanyshev N, Adamo GM, Porro D, Branduardi P. The spoilage yeastZygosaccharomyces bailii: Foe or friend? Yeast 2017; 34:359-370. [DOI: 10.1002/yea.3238] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 05/12/2017] [Accepted: 05/15/2017] [Indexed: 12/30/2022] Open
Affiliation(s)
- Nurzhan Kuanyshev
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 Milano 20126 Italy
| | - Giusy M. Adamo
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 Milano 20126 Italy
| | - Danilo Porro
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 Milano 20126 Italy
| | - Paola Branduardi
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 Milano 20126 Italy
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38
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Benocci T, Aguilar-Pontes MV, Zhou M, Seiboth B, de Vries RP. Regulators of plant biomass degradation in ascomycetous fungi. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:152. [PMID: 28616076 PMCID: PMC5468973 DOI: 10.1186/s13068-017-0841-x] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/06/2017] [Indexed: 05/05/2023]
Abstract
Fungi play a major role in the global carbon cycle because of their ability to utilize plant biomass (polysaccharides, proteins, and lignin) as carbon source. Due to the complexity and heterogenic composition of plant biomass, fungi need to produce a broad range of degrading enzymes, matching the composition of (part of) the prevalent substrate. This process is dependent on a network of regulators that not only control the extracellular enzymes that degrade the biomass, but also the metabolic pathways needed to metabolize the resulting monomers. This review will summarize the current knowledge on regulation of plant biomass utilization in fungi and compare the differences between fungal species, focusing in particular on the presence or absence of the regulators involved in this process.
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Affiliation(s)
- Tiziano Benocci
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Maria Victoria Aguilar-Pontes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Miaomiao Zhou
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Bernhard Seiboth
- Research Area Biochemical Technology, Institute of Chemical and Biological Engineering, TU Wien, 1060 Vienna, Austria
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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39
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Teerapatsakul C, Chitradon L. Physiological Regulation of an Alkaline-Resistant Laccase Produced by Perenniporia tephropora and Efficiency in Biotreatment of Pulp Mill Effluent. MYCOBIOLOGY 2016; 44:260-268. [PMID: 28154483 PMCID: PMC5287158 DOI: 10.5941/myco.2016.44.4.260] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 08/21/2016] [Accepted: 09/19/2016] [Indexed: 05/31/2023]
Abstract
Regulation of alkaline-resistant laccase from Perenniporia tephropora KU-Alk4 was proved to be controlled by several factors. One important factor was the initial pH, which drove the fungus to produce different kinds of ligninolytic enzymes. P. tephropora KU-Alk4 could grow at pH 4.5, 7.0, and 8.0. The fungus produced laccase and MnP at pH 7.0, but only laccase at pH 8.0. The specific activity of laccase in the pH 8.0 culture was higher than that in the pH 7.0 culture. At pH 8.0, glucose was the best carbon source for laccase production but growth was better with lactose. Low concentrations of glucose at 0.1% to 1.0% enhanced laccase production, while concentrations over 1% gave contradictory results. Veratryl alcohol induced the production of laccase. A trace concentration of copper ions was required for laccase production. Biomass increased with an increasing rate of aeration of shaking flasks from 100 to 140 rpm; however, shaking at over 120 rpm decreased laccase quantity. Highest amount of laccase produced by KU-Alk4, 360 U/mL, was at pH 8.0 with 1% glucose and 0.2 mM copper sulfate, unshaken for the first 3 days, followed by addition of 0.85 mM veratryl alcohol and shaking at 120 rpm. The crude enzyme was significantly stable in alkaline pH 8.0~10.0 for 24 hr. After treating the pulp mill effluent with the KU-Alk4 system for 3 days, pH decreased from 9.6 to 6.8, with reduction of color and chemical oxygen demand at 83.2% and 81%, respectively. Laccase was detectable during the biotreatment process.
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Affiliation(s)
- Churapa Teerapatsakul
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.; Center for Advanced Studies in Tropical Natural Resources, Kasetsart University, Bangkok 10900, Thailand
| | - Lerluck Chitradon
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.; Center for Advanced Studies in Tropical Natural Resources, Kasetsart University, Bangkok 10900, Thailand
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40
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Cambri G, de Sousa MML, Fonseca DDM, Marchini FK, da Silveira JLM, Paba J. Analysis of the Biotechnological Potential of a Lentinus crinitus Isolate in the Light of Its Secretome. J Proteome Res 2016; 15:4557-4568. [DOI: 10.1021/acs.jproteome.6b00636] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Geison Cambri
- Departamento
de Bioquímica, Setor de Ciências Biológicas,
Centro Politécnico, Universidade Federal do Paraná, 81531-990 Curitiba-PR, Brazil
| | - Mirta Mittelstedt Leal de Sousa
- Department
of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NTNU, N-7491 Trondheim, Norway
| | - Davi de Miranda Fonseca
- Department
of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NTNU, N-7491 Trondheim, Norway
- Proteomics
and Metabolomics Core Facility (PROMEC), Norwegian University of Science and Technology, NTNU, N-7491 Trondheim, Norway
| | - Fabricio K. Marchini
- Laboratório
de Genômica Funcional, Instituto Carlos Chagas, Fundação Oswaldo Cruz, 81350-010 Curitiba-PR, Brazil
| | - Joana Lea Meira da Silveira
- Departamento
de Bioquímica, Setor de Ciências Biológicas,
Centro Politécnico, Universidade Federal do Paraná, 81531-990 Curitiba-PR, Brazil
| | - Jaime Paba
- Departamento
de Bioquímica, Setor de Ciências Biológicas,
Centro Politécnico, Universidade Federal do Paraná, 81531-990 Curitiba-PR, Brazil
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41
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Spina F, Junghanns C, Donelli I, Nair R, Demarche P, Romagnolo A, Freddi G, Agathos SN, Varese GC. Stimulation of laccases from Trametes pubescens: Use in dye decolorization and cotton bleaching. Prep Biochem Biotechnol 2016; 46:639-47. [DOI: 10.1080/10826068.2015.1128445] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Federica Spina
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Charles Junghanns
- Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Ilaria Donelli
- Divisione Stazione Sperimentale per la Seta, Innovhub-SSI, Milano, Italy
| | - Rakesh Nair
- Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Philippe Demarche
- Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Alice Romagnolo
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Giuliano Freddi
- Divisione Stazione Sperimentale per la Seta, Innovhub-SSI, Milano, Italy
| | - Spiros N. Agathos
- Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
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42
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Braunsdorf C, Mailänder-Sánchez D, Schaller M. Fungal sensing of host environment. Cell Microbiol 2016; 18:1188-200. [DOI: 10.1111/cmi.12610] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/02/2016] [Accepted: 05/05/2016] [Indexed: 12/13/2022]
Affiliation(s)
- C. Braunsdorf
- Department of Dermatology; University Hospital Tübingen; Liebermeisterstr. 25 Tübingen Germany
| | - D. Mailänder-Sánchez
- Department of Internal Medicine I; University Hospital Tübingen; Otfried-Müller-Straße 10 72076 Tübingen
| | - M. Schaller
- Department of Dermatology; University Hospital Tübingen; Liebermeisterstr. 25 Tübingen Germany
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43
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Yang L, Lübeck M, Souroullas K, Lübeck PS. Co-consumption of glucose and xylose for organic acid production by Aspergillus carbonarius cultivated in wheat straw hydrolysate. World J Microbiol Biotechnol 2016; 32:57. [PMID: 26925619 DOI: 10.1007/s11274-016-2025-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 02/04/2016] [Indexed: 12/01/2022]
Abstract
Aspergillus carbonarius exhibits excellent abilities to utilize a wide range of carbon sources and to produce various organic acids. In this study, wheat straw hydrolysate containing high concentrations of glucose and xylose was used for organic acid production by A. carbonarius. The results indicated that A. carbonarius efficiently co-consumed glucose and xylose and produced various types of organic acids in hydrolysate adjusted to pH 7. The inhibitor tolerance of A. carbonarius to the hydrolysate at different pH values was investigated and compared using spores and recycled mycelia. This comparison showed a slight difference in the inhibitor tolerance of the spores and the recycled mycelia based on their growth patterns. Moreover, the wild-type and a glucose oxidase deficient (Δgox) mutant were compared for their abilities to produce organic acids using the hydrolysate and a defined medium. The two strains showed a different pattern of organic acid production in the hydrolysate where the Δgox mutant produced more oxalic acid but less citric acid than the wild-type, which was different from the results obtained in the defined medium This study demonstrates the feasibility of using lignocellulosic biomass for the organic acid production by A. carbonarius.
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Affiliation(s)
- Lei Yang
- Section for Sustainable Biotechnology, Department of Chemistry and Bioscience, Aalborg University Copenhagen, A. C. Meyers Vaenge 15, 2450, Copenhagen SV, Denmark
| | - Mette Lübeck
- Section for Sustainable Biotechnology, Department of Chemistry and Bioscience, Aalborg University Copenhagen, A. C. Meyers Vaenge 15, 2450, Copenhagen SV, Denmark
| | - Konstantinos Souroullas
- Section for Sustainable Biotechnology, Department of Chemistry and Bioscience, Aalborg University Copenhagen, A. C. Meyers Vaenge 15, 2450, Copenhagen SV, Denmark.,MEDOCHEMIE LTD, 1-10 Constantinoupoleos St., 3011, Limassol, Cyprus
| | - Peter S Lübeck
- Section for Sustainable Biotechnology, Department of Chemistry and Bioscience, Aalborg University Copenhagen, A. C. Meyers Vaenge 15, 2450, Copenhagen SV, Denmark.
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44
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The Renaissance of Neurospora crassa: How a Classical Model System is Used for Applied Research. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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45
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Rineau F, Stas J, Nguyen NH, Kuyper TW, Carleer R, Vangronsveld J, Colpaert JV, Kennedy PG. Ectomycorrhizal Fungal Protein Degradation Ability Predicted by Soil Organic Nitrogen Availability. Appl Environ Microbiol 2015; 82:1391-1400. [PMID: 26682855 PMCID: PMC4771325 DOI: 10.1128/aem.03191-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 12/04/2015] [Indexed: 11/20/2022] Open
Abstract
In temperate and boreal forest ecosystems, nitrogen (N) limitation of tree metabolism is alleviated by ectomycorrhizal (ECM) fungi. As forest soils age, the primary source of N in soil switches from inorganic (NH4 (+) and NO3 (-)) to organic (mostly proteins). It has been hypothesized that ECM fungi adapt to the most common N source in their environment, which implies that fungi growing in older forests would have greater protein degradation abilities. Moreover, recent results for a model ECM fungal species suggest that organic N uptake requires a glucose supply. To test the generality of these hypotheses, we screened 55 strains of 13 Suillus species with different ecological preferences for their in vitro protein degradation abilities. Suillus species preferentially occurring in mature forests, where soil contains more organic matter, had significantly higher protease activity than those from young forests with low-organic-matter soils or species indifferent to forest age. Within species, the protease activities of ecotypes from soils with high or low soil organic N content did not differ significantly, suggesting resource partitioning between mineral and organic soil layers. The secreted protease mixtures were strongly dominated by aspartic peptidases. Glucose addition had variable effects on secreted protease activity; in some species, it triggered activity, but in others, activity was repressed at high concentrations. Collectively, our results indicate that protease activity, a key ectomycorrhizal functional trait, is positively related to environmental N source availability but is also influenced by additional factors, such as carbon availability.
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Affiliation(s)
- Francois Rineau
- Centre for Environmental Sciences, Environmental Biology Group, Hasselt University, Hasselt, Belgium
| | - Jelle Stas
- Centre for Environmental Sciences, Environmental Biology Group, Hasselt University, Hasselt, Belgium
| | - Nhu H Nguyen
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Thomas W Kuyper
- Department of Soil Quality, Wageningen University, Wageningen, The Netherlands
| | - Robert Carleer
- Centre for Environmental Sciences, Environmental Biology Group, Hasselt University, Hasselt, Belgium
| | - Jaco Vangronsveld
- Centre for Environmental Sciences, Environmental Biology Group, Hasselt University, Hasselt, Belgium
| | - Jan V Colpaert
- Centre for Environmental Sciences, Environmental Biology Group, Hasselt University, Hasselt, Belgium
| | - Peter G Kennedy
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota, USA
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46
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You J, Liu JF, Yang SZ, Mu BZ. Low-temperature-active and salt-tolerant β-mannanase from a newly isolated Enterobacter sp. strain N18. J Biosci Bioeng 2015; 121:140-6. [PMID: 26168907 DOI: 10.1016/j.jbiosc.2015.06.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 05/21/2015] [Accepted: 06/06/2015] [Indexed: 02/05/2023]
Abstract
A low-temperature-active and salt-tolerant β-mannanase produced by a novel mannanase-producer, Enterobacter sp. strain N18, was isolated, purified and then evaluated for its potential application as a gel-breaker in relation to viscosity reduction of guar-based hydraulic fracturing fluids used in oil field. The enzyme could lower the viscosity of guar gum solution by more than 95% within 10 min. The purified β-mannanase with molecular mass of 90 kDa displayed high activity in a broad range of pH and temperature: more than 70% of activity was retained in the pH range of 3.0-8.0 with the optimal pH 7.5, about 50% activity at 20°C with the optimal temperature 50°C. Furthermore, the enzyme retained >70% activity in the presence of 0.5-4.0 M NaCl. These properties implied that the enzyme from strain N18 had potential for serving as a gel-breaker for low temperature oil wells and other industrial fields, where chemical gel breakers were inactive due to low temperature.
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Affiliation(s)
- Jia You
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, Shanghai 200237, PR China
| | - Jin-Feng Liu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, Shanghai 200237, PR China
| | - Shi-Zhong Yang
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, Shanghai 200237, PR China
| | - Bo-Zhong Mu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, Shanghai 200237, PR China; Collaborative Innovation Center for Biomanufacturing Technology, Shanghai 200237, PR China.
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47
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Almeida SM, Umeo SH, Marcante RC, Yokota ME, Valle JS, Dragunski DC, Colauto NB, Linde GA. Iron bioaccumulation in mycelium of Pleurotus ostreatus. Braz J Microbiol 2015. [PMID: 26221108 PMCID: PMC4512064 DOI: 10.1590/s1517-838246120130695] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Pleurotus ostreatus
is able to bioaccumulate several metals in its cell structures; however, there are no reports on its capacity to bioaccumulate iron. The objective of this study was to evaluate cultivation variables to increase iron bioaccumulation in P. ostreatus
mycelium. A full factorial design and a central composite design were utilized to evaluate the effect of the following variables: nitrogen and carbon sources, pH and iron concentration in the solid culture medium to produce iron bioaccumulated in mycelial biomass. The maximum production of P. ostreatus
mycelial biomass was obtained with yeast extract at 2.96 g of nitrogen L
−1
and glucose at 28.45 g L
−1
. The most important variable to bioaccumulation was the iron concentration in the cultivation medium. Iron concentration at 175 mg L
−1
or higher in the culture medium strongly inhibits the mycelial growth. The highest iron concentration in the mycelium was 3500 mg kg
−1
produced with iron addition of 300 mg L
−1
. The highest iron bioaccumulation in the mycelium was obtained in culture medium with 150 mg L
−1
of iron. Iron bioaccumulation in P. ostreatus
mycelium is a potential alternative to produce non-animal food sources of iron.
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Affiliation(s)
- Sandra M Almeida
- Laboratório de Biologia Molecular, Universidade Paranaense, Umuarama, PR, Brazil
| | - Suzana H Umeo
- Laboratório de Biologia Molecular, Universidade Paranaense, Umuarama, PR, Brazil
| | - Rafael C Marcante
- Laboratório de Biologia Molecular, Universidade Paranaense, Umuarama, PR, Brazil
| | - Meire E Yokota
- Laboratório de Biologia Molecular, Universidade Paranaense, Umuarama, PR, Brazil
| | - Juliana S Valle
- Laboratório de Biologia Molecular, Universidade Paranaense, Umuarama, PR, Brazil
| | | | - Nelson B Colauto
- Laboratório de Biologia Molecular, Universidade Paranaense, Umuarama, PR, Brazil
| | - Giani A Linde
- Laboratório de Biologia Molecular, Universidade Paranaense, Umuarama, PR, Brazil
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49
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Yao G, Li Z, Gao L, Wu R, Kan Q, Liu G, Qu Y. Redesigning the regulatory pathway to enhance cellulase production in Penicillium oxalicum. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:71. [PMID: 25949521 PMCID: PMC4422585 DOI: 10.1186/s13068-015-0253-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/09/2015] [Indexed: 05/05/2023]
Abstract
BACKGROUND In cellulolytic fungi, induction and repression mechanisms synchronously regulate the synthesis of cellulolytic enzymes for accurate responses to carbon sources in the environment. Many proteins, particularly transcription regulatory factors involved in these processes, were identified and genetically engineered in Penicillium oxalicum and other cellulolytic fungi. Despite such great efforts, its effect of modifying a single target to improve the production of cellulase is highly limited. RESULTS In this study, we developed a systematic strategy for the genetic engineering of P. oxalicum to enhance cellulase yields, by enhancing induction (by blocking intracellular inducer hydrolysis and increasing the activator level) and relieving the repression. We obtained a trigenic recombinant strain named 'RE-10' by deleting bgl2 and creA, along with over-expressing the gene clrB. The cellulolytic ability of RE-10 was significantly improved; the filter paper activity and extracellular protein concentration increased by up to over 20- and 10-fold, respectively, higher than those of the wild-type (WT) strain 114-2 both on pure cellulose and complex wheat bran media. Most strikingly, the cellulolytic ability of RE-10 was comparable with that of the industrial P. oxalicum strain JU-A10-T obtained by random mutagenesis. Comparative proteomics analysis provided further insights into the differential secretomes between RE-10 and WT strains. In particular, the enzymes and accessory proteins involved in lignocellulose degradation were elevated specifically and dramatically in the recombinant, thereby confirming the importance of them in biomass deconstruction and implying a possible co-regulatory mechanism. CONCLUSIONS We established a novel route to substantially improve cellulolytic enzyme production up to the industrial level in P. oxalicum by combinational manipulation of three key genes to amplify the induction along with derepression, representing a milestone in strain engineering of filamentous fungi. Given the conservation in the mode of cellulose expression regulation among filamentous fungi, this strategy could be compatible with other cellulase-producing fungi.
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Affiliation(s)
- Guangshan Yao
- />State Key Laboratory of Microbial Technology, Shandong University, Jinan City, Shandong Province 250100 China
| | - Zhonghai Li
- />State Key Laboratory of Microbial Technology, Shandong University, Jinan City, Shandong Province 250100 China
- />Qingdao Vland Biotech Group Co. Ltd., Shandong Expressway Mansion, Miaoling Road, Qingdao, Shandong China
| | - Liwei Gao
- />State Key Laboratory of Microbial Technology, Shandong University, Jinan City, Shandong Province 250100 China
| | - Ruimei Wu
- />State Key Laboratory of Microbial Technology, Shandong University, Jinan City, Shandong Province 250100 China
| | - Qinbiao Kan
- />State Key Laboratory of Microbial Technology, Shandong University, Jinan City, Shandong Province 250100 China
| | - Guodong Liu
- />State Key Laboratory of Microbial Technology, Shandong University, Jinan City, Shandong Province 250100 China
| | - Yinbo Qu
- />State Key Laboratory of Microbial Technology, Shandong University, Jinan City, Shandong Province 250100 China
- />National Glycoengineering Research Center, Shandong University, Jinan City, Shandong Province 250100 China
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Li D, Yan Z, Lu L, Jiang H, Wang W. Pleiotropy of the de novo-originated gene MDF1. Sci Rep 2014; 4:7280. [PMID: 25452167 PMCID: PMC4250933 DOI: 10.1038/srep07280] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 11/11/2014] [Indexed: 12/20/2022] Open
Abstract
MDF1 is a young de novo-originated gene from a non-coding sequence in baker's yeast, S. cerevisiae, which can suppress mating and promote vegetative growth. Our previous experiments successfully demonstrated how Mdf1p binds to the key mating pathway determinant MATα2 to suppress mating. However, how Mdf1p promotes growth and fulfills the crosstalk between the yeast mating and growth pathways are still open questions. Thus, the adaptive significance of this new de novo gene remains speculative. Here, we show that Mdf1p shortens the lag phase of S. cerevisiae by physically interacting with SNF1, the governing factor for nonfermentable carbon source utilization, and thereby confers a selective advantage on yeasts through the rapid consumption of glucose in the early generational stage in rich medium. Therefore, MDF1 functions in two important molecular pathways, mating and fermentation, and mediates the crosstalk between reproduction and vegetative growth. Together, our results provide a comprehensive example of how a de novo-originated gene organizes new regulatory circuits and thereby confers a selective advantage on S. cerevisiae to allow exquisite adaptation to the changing environment.
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Affiliation(s)
- Dan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, People's Republic of China
| | - Zhihui Yan
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences(CAS), Tianjin 300308, People's Republic of China
| | - Lina Lu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences(CAS), Tianjin 300308, People's Republic of China
| | - Huifeng Jiang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences(CAS), Tianjin 300308, People's Republic of China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, People's Republic of China
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