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Oliveira BR, Marques AP, Ressurreição M, Moreira CJS, S Pereira C, B Crespo MT, Pereira VJ. Inactivation of Aspergillus species in real water matrices using medium pressure mercury lamps. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2021; 221:112242. [PMID: 34214837 DOI: 10.1016/j.jphotobiol.2021.112242] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/12/2021] [Accepted: 06/10/2021] [Indexed: 11/16/2022]
Abstract
The aim of this work is to understand the inactivation efficiency of medium pressure mercury lamps, measured in terms of growth inhibition as well as cell death, damage and response, using three strains from three different Aspergillus species (A. fumigatus, A. niger and, A. terreus) spiked in filtered surface water. A complete characterization of the effect of the treatment on each strain of the fungal species was assessed considering spores' morphology, cell wall integrity and enzymatic activity, the formation of pyrimidine dimers in the DNA and proteome analysis. Results showed that, when subjected to medium pressure mercury lamps, A. niger is the most resistant to inactivation, that both A. fumigatus and A. niger suffer more morphological changes and present a higher number of damaged spores and A. terreus presented more dead spores. DNA damages detected in A. niger were able to be repaired to some extent, under both light and dark conditions. Finally, proteome analysis showed that the UV radiation treatment triggered different types of stress response, including cell wall reorganization and DNA repair in A. fumigatus and A. terreus, and oxidative stress responses like the increase in production of citric acid and itaconic acid in A. niger and A. terreus, respectively.
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Affiliation(s)
- B R Oliveira
- iBET - Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780-901 Oeiras, Portugal; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - A P Marques
- iBET - Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780-901 Oeiras, Portugal
| | - M Ressurreição
- iBET - Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780-901 Oeiras, Portugal
| | - C J S Moreira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - C S Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - M T B Crespo
- iBET - Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780-901 Oeiras, Portugal; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - V J Pereira
- iBET - Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780-901 Oeiras, Portugal; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
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103
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Current Promising Therapeutic Targets for Aspergillosis Treatment. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.2.09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aspergillosis is a fungal disease caused by different species of Aspergillus. They live in soil,dust and decomposed material. Number of Aspergillus species found till now is about 300 and more are still to be identified. Only few Aspergillus species can cause human disease and the most common species for human infection is Aspergillus fumigatus, which is a ubiquitous airborne saprophytic fungus. Severity of the disease ranges from an allergic response to life-threatening generalized infection. They grow optimally at 37°C and can grow upto 50°C. The fungal conidia are being constantly inhaled by humans and animals everyday normally gets eliminated by innate immune mechanism. Due to increasing number of immunocompromised patients, severe and fatal Aspergillosis cases have augmented. Currently, available antifungal drug for the treatment of Aspergillosis act on these three molecular target are 14 alpha demethylase for Azoles, ergosterol for Polyene and β-1,3-glucan synthase for Echinocandin. These antifungal drug show high resistance problem and toxicity. So, it is high time to develop new drugs for treatment with reduced toxicity and drug resistant problem. Synthesis of essential amino acid is absent in human as they obtain it from their diet but fungi synthesis these amino acid. Thus, enzymes in this pathway acts as novel drug target. This article summarizes promising drug targets presents in different metabolic pathway of Aspergillus genome and discusses their molecular functions in detail. This review also list down the inhibitors of these novel target. We present a comprehensive review that will pave way for discovery and development of novel antifungals against these drug targets for Aspergillosis treatment.
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104
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Hage H, Rosso MN, Tarrago L. Distribution of methionine sulfoxide reductases in fungi and conservation of the free-methionine-R-sulfoxide reductase in multicellular eukaryotes. Free Radic Biol Med 2021; 169:187-215. [PMID: 33865960 DOI: 10.1016/j.freeradbiomed.2021.04.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/17/2022]
Abstract
Methionine, either as a free amino acid or included in proteins, can be oxidized into methionine sulfoxide (MetO), which exists as R and S diastereomers. Almost all characterized organisms possess thiol-oxidoreductases named methionine sulfoxide reductase (Msr) enzymes to reduce MetO back to Met. MsrA and MsrB reduce the S and R diastereomers of MetO, respectively, with strict stereospecificity and are found in almost all organisms. Another type of thiol-oxidoreductase, the free-methionine-R-sulfoxide reductase (fRMsr), identified so far in prokaryotes and a few unicellular eukaryotes, reduces the R MetO diastereomer of the free amino acid. Moreover, some bacteria possess molybdenum-containing enzymes that reduce MetO, either in the free or protein-bound forms. All these Msrs play important roles in the protection of organisms against oxidative stress. Fungi are heterotrophic eukaryotes that colonize all niches on Earth and play fundamental functions, in organic matter recycling, as symbionts, or as pathogens of numerous organisms. However, our knowledge on fungal Msrs is still limited. Here, we performed a survey of msr genes in almost 700 genomes across the fungal kingdom. We show that most fungi possess one gene coding for each type of methionine sulfoxide reductase: MsrA, MsrB, and fRMsr. However, several fungi living in anaerobic environments or as obligate intracellular parasites were devoid of msr genes. Sequence inspection and phylogenetic analyses allowed us to identify non-canonical sequences with potentially novel enzymatic properties. Finaly, we identified several ocurences of msr horizontal gene transfer from bacteria to fungi.
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Affiliation(s)
- Hayat Hage
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France
| | - Marie-Noëlle Rosso
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France
| | - Lionel Tarrago
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France.
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105
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Arentshorst M, Falco MD, Moisan MC, Reid ID, Spaapen TOM, van Dam J, Demirci E, Powlowski J, Punt PJ, Tsang A, Ram AFJ. Identification of a Conserved Transcriptional Activator-Repressor Module Controlling the Expression of Genes Involved in Tannic Acid Degradation and Gallic Acid Utilization in Aspergillus niger. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:681631. [PMID: 37744122 PMCID: PMC10512348 DOI: 10.3389/ffunb.2021.681631] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/23/2021] [Indexed: 09/26/2023]
Abstract
Tannic acid, a hydrolysable gallotannin present in plant tissues, consists of a central glucose molecule esterified with gallic acid molecules. Some microorganisms, including several Aspergillus species, can metabolize tannic acid by releasing gallic acid residues from tannic acid by secreting tannic acid specific esterases into the medium. The expression of these so-called tannases is induced by tannic acid or gallic acid. In this study, we identified a conserved transcriptional activator-repressor module involved in the regulation of predicted tannases and other genes involved in gallic acid metabolism. The transcriptional activator-repressor module regulating tannic acid utilization resembles the transcriptional activator-repressor modules regulating galacturonic acid and quinic acid utilization. Like these modules, the Zn(II)2Cys6 transcriptional activator (TanR) and the putative repressor (TanX) are located adjacent to each other. Deletion of the transcriptional activator (ΔtanR) results in inability to grow on gallic acid and severely reduces growth on tannic acid. Deletion of the putative repressor gene (ΔtanX) results in the constitutive expression of tannases as well as other genes with mostly unknown function. Known microbial catabolic pathways for gallic acid utilization involve so-called ring cleavage enzymes, and two of these ring cleavage enzymes show increased expression in the ΔtanX mutant. However, deletion of these two genes, and even deletion of all 17 genes encoding potential ring cleavage enzymes, did not result in a gallic acid non-utilizing phenotype. Therefore, in A. niger gallic acid utilization involves a hitherto unknown pathway. Transcriptome analysis of the ΔtanX mutant identified several genes and gene clusters that were significantly induced compared to the parental strain. The involvement of a selection of these genes and gene clusters in gallic acid utilization was examined by constructing gene deletion mutants and testing their ability to grow on gallic acid. Only the deletion of a gene encoding an FAD-dependent monooxygenase (NRRL3_04659) resulted in a strain that was unable to grow on gallic acid. Metabolomic studies showed accumulation of gallic acid in the ΔNRRL3_04659 mutant suggesting that this predicted monooxygenase is involved in the first step of gallic acid metabolism and is likely responsible for oxidation of the aromatic ring.
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Affiliation(s)
- Mark Arentshorst
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Marcos Di Falco
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Marie-Claude Moisan
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Ian D. Reid
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Tessa O. M. Spaapen
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Jisca van Dam
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Ebru Demirci
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Justin Powlowski
- Department of Chemistry & Biochemistry, Concordia University, Montreal, QC, Canada
| | - Peter J. Punt
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
- Dutch DNA Biotech, Hugo R Kruytgebouw 4-Noord, Utrecht, Netherlands
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Arthur F. J. Ram
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
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Laothanachareon T, Bruinsma L, Nijsse B, Schonewille T, Suarez-Diez M, Tamayo-Ramos JA, Martins dos Santos VAP, Schaap PJ. Global Transcriptional Response of Aspergillus niger to Blocked Active Citrate Export through Deletion of the Exporter Gene. J Fungi (Basel) 2021; 7:jof7060409. [PMID: 34071072 PMCID: PMC8224569 DOI: 10.3390/jof7060409] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/21/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022] Open
Abstract
Aspergillus niger is the major industrial citrate producer worldwide. Export as well as uptake of citric acid are believed to occur by active, proton-dependent, symport systems. Both are major bottlenecks for industrial citrate production. Therefore, we assessed the consequences of deleting the citT gene encoding the A. niger citrate exporter, effectively blocking active citrate export. We followed the consumption of glucose and citrate as carbon sources, monitored the secretion of organic acids and carried out a thorough transcriptome pathway enrichment analysis. Under controlled cultivation conditions that normally promote citrate secretion, the knock-out strain secreted negligible amounts of citrate. Blocking active citrate export in this way led to a reduced glucose uptake and a reduced expression of high-affinity glucose transporter genes, mstG and mstH. The glyoxylate shunt was strongly activated and an increased expression of the OAH gene was observed, resulting in a more than two-fold higher concentration of oxalate in the medium. Deletion of citT did not affect citrate uptake suggesting that citrate export and citrate uptake are uncoupled from the system.
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Affiliation(s)
- Thanaporn Laothanachareon
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
- Enzyme Technology Laboratory, Biorefinery and Bioproduct Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Khlong Luang, Pathumthani 12120, Thailand
- Correspondence: (T.L.); (V.A.P.M.d.S.)
| | - Lyon Bruinsma
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
| | - Bart Nijsse
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
| | - Tom Schonewille
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
| | - Juan Antonio Tamayo-Ramos
- International Research Center in Critical Raw Materials-ICCRAM, University of Burgos, 09001 Burgos, Spain;
| | - Vitor A. P. Martins dos Santos
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
- LifeGlimmer GmbH, 12163 Berlin, Germany
- Correspondence: (T.L.); (V.A.P.M.d.S.)
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (L.B.); (B.N.); (T.S.); (M.S.-D.); (P.J.S.)
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107
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The pentose phosphate pathway in industrially relevant fungi: crucial insights for bioprocessing. Appl Microbiol Biotechnol 2021; 105:4017-4031. [PMID: 33950280 PMCID: PMC8140973 DOI: 10.1007/s00253-021-11314-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/04/2021] [Accepted: 04/20/2021] [Indexed: 11/12/2022]
Abstract
Abstract The pentose phosphate pathway (PPP) is one of the most targeted pathways in metabolic engineering. This pathway is the primary source of NADPH, and it contributes in fungi to the production of many compounds of interest such as polyols, biofuels, carotenoids, or antibiotics. However, the regulatory mechanisms of the PPP are still not fully known. This review provides an insight into the current comprehension of the PPP in fungi and the limitations of this current understanding. It highlights how this knowledge contributes to targeted engineering of the PPP and thus to better performance of industrially used fungal strains. Key points • Type of carbon and nitrogen source as well as oxidative stress influence the PPP. • A complex network of transcription factors regulates the PPP. • Improved understanding of the PPP will allow to increase yields of bioprocesses.
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108
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Demirci E, Arentshorst M, Yilmaz B, Swinkels A, Reid ID, Visser J, Tsang A, Ram AFJ. Genetic Characterization of Mutations Related to Conidiophore Stalk Length Development in Aspergillus niger Laboratory Strain N402. Front Genet 2021; 12:666684. [PMID: 33959152 PMCID: PMC8093798 DOI: 10.3389/fgene.2021.666684] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/29/2021] [Indexed: 11/29/2022] Open
Abstract
Aspergillus niger is an important filamentous fungus in industrial biotechnology for the production of citric acid and enzymes. In the late 1980s, the A. niger N400/NRRL3 strain was selected for both fundamental and applied studies in relation to several processes including gluconic acid and protein production. To facilitate handling of A. niger, the N400 wild-type strain was UV mutagenized in two consecutive rounds to generate N401 and N402. N402 was used as a reference laboratory strain and exhibits the phenotypes with reduced conidiophore stalk length and reduced radial growth. The conidiophore stalk length and radial growth of A. niger strain N400 were determined and compared to N401 and N402. The length of N400 conidiophore stalks (2.52 ± 0.40 mm) was reduced in N401 and N402 to 0.66 ± 0.14 mm and 0.34 ± 0.06 mm, respectively. Whereas N400 reached a colony diameter of 6.7 ± 0.2 cm after 7 days, N401 and N402 displayed reduced radial growth phenotype (4.3 ± 0.1 and 4.1 ± 0.1, respectively). To identify the mutations (dubbed cspA and cspB) responsible for the phenotypes of N401 and N402, the genomes were sequenced and compared to the N400 genome sequence. A parasexual cross was performed between N400 and N402 derivatives to isolate segregants which allowed cosegregation analysis of single nucleotide polymorphisms and insertions and deletions among the segregants. The shorter conidiophore stalk and reduced radial growth in N401 (cspA) was found to be caused by a 9-kb deletion on chromosome III and was further narrowed down to a truncation of NRRL3_03857 which encodes a kinesin-like protein homologous to the A. nidulans UncA protein. The mutation responsible for the further shortening of conidiophore stalks in N402 (cspB) was found to be caused by a missense mutation on chromosome V in a hitherto unstudied C2H2 transcription factor encoded by the gene NRRL3_06646. The importance of these two genes in relation to conidiophore stalk length and radial growth was confirmed by single and double gene deletion studies. The mutations in the laboratory strain N402 should be taken into consideration when studying phenotypes in the N402 background.
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Affiliation(s)
- Ebru Demirci
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Leiden, Netherlands
| | - Mark Arentshorst
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Leiden, Netherlands
| | - Baran Yilmaz
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Leiden, Netherlands
| | - Aram Swinkels
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Leiden, Netherlands
| | - Ian D Reid
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Jaap Visser
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Leiden, Netherlands.,Fungal Genetics and Technology Consultancy, Wageningen, Netherlands
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Arthur F J Ram
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Leiden, Netherlands
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109
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Kumar S, Mutturi S. Alternative splicing regulates the α-glucosidase synthesis in Aspergillus neoniger NCIM 1400. Fungal Biol 2021; 125:658-665. [PMID: 34281659 DOI: 10.1016/j.funbio.2021.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 02/26/2021] [Accepted: 04/07/2021] [Indexed: 10/21/2022]
Abstract
Aspergillus neoniger NCIM 1400 whose cell-free fraction was earlier established for transglycosylation activity conferred by α-glucosidase gene (agdA), was subjected to sequence analysis. Preliminary results revealed certain dynamics in the intron splicing mechanism, and to ascertain these molecular events, a detailed study was carried. The electrophoresis results from the cDNA portion (B-fragment) of agdA showed multiple bands, indicating the amplification of one or more fragments. The sequence results of cDNA cloned vector revealed the retention type of alternative splicing in the agdA. The splicing mechanism of agdA in NCIM 1400 was compared to different A. niger strains, which harbours agdA orthologues, using PCR. It was observed that effective intron splicing leads to higher α-glucosidase activity from these selected Aspergillus spp. To explore the dynamics of intron retention in A. neoniger NCIM 1400, time-course analysis of intron retention, enzyme activity, and sugar consumption were carried over a period of 168 h of fungal growth. RT-qPCR results revealed that introns retention was not detected during the initial growth phase when the maltose and its hydrolysed product, glucose were consumed. Here we demonstrate that exhaustion of maltose causes increase in retention of introns in the mRNA transcripts of agdA gene, and this could be the possible mode of regulating this gene.
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Affiliation(s)
- Sandeep Kumar
- Microbiology & Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka, 570020, India; AcSIR-Academy of Scientific & Innovative Research, Ghaziabad, UP, 201002, India
| | - Sarma Mutturi
- Microbiology & Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka, 570020, India; AcSIR-Academy of Scientific & Innovative Research, Ghaziabad, UP, 201002, India.
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110
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Baltussen TJH, Coolen JPM, Verweij PE, Dijksterhuis J, Melchers WJG. Identifying Conserved Generic Aspergillus spp. Co-Expressed Gene Modules Associated with Germination Using Cross-Platform and Cross-Species Transcriptomics. J Fungi (Basel) 2021; 7:270. [PMID: 33916245 PMCID: PMC8067318 DOI: 10.3390/jof7040270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/27/2021] [Accepted: 03/29/2021] [Indexed: 12/26/2022] Open
Abstract
Aspergillus spp. is an opportunistic human pathogen that may cause a spectrum of pulmonary diseases. In order to establish infection, inhaled conidia must germinate, whereby they break dormancy, start to swell, and initiate a highly polarized growth process. To identify critical biological processes during germination, we performed a cross-platform, cross-species comparative analysis of germinating A. fumigatus and A. niger conidia using transcriptional data from published RNA-Seq and Affymetrix studies. A consensus co-expression network analysis identified four gene modules associated with stages of germination. These modules showed numerous shared biological processes between A. niger and A. fumigatus during conidial germination. Specifically, the turquoise module was enriched with secondary metabolism, the black module was highly enriched with protein synthesis, the darkgreen module was enriched with protein fate, and the blue module was highly enriched with polarized growth. More specifically, enriched functional categories identified in the blue module were vesicle formation, vesicular transport, tubulin dependent transport, actin-dependent transport, exocytosis, and endocytosis. Genes important for these biological processes showed similar expression patterns in A. fumigatus and A. niger, therefore, they could be potential antifungal targets. Through cross-platform, cross-species comparative analysis, we were able to identify biologically meaningful modules shared by A. fumigatus and A. niger, which underscores the potential of this approach.
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Affiliation(s)
- Tim J. H. Baltussen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (J.P.M.C.); (P.E.V.); (W.J.G.M.)
- Center of Expertise in Mycology Radboudumc/CWZ, 6532 SZ Nijmegen, The Netherlands
| | - Jordy P. M. Coolen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (J.P.M.C.); (P.E.V.); (W.J.G.M.)
- Center of Expertise in Mycology Radboudumc/CWZ, 6532 SZ Nijmegen, The Netherlands
| | - Paul E. Verweij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (J.P.M.C.); (P.E.V.); (W.J.G.M.)
- Center of Expertise in Mycology Radboudumc/CWZ, 6532 SZ Nijmegen, The Netherlands
| | - Jan Dijksterhuis
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (J.P.M.C.); (P.E.V.); (W.J.G.M.)
- Center of Expertise in Mycology Radboudumc/CWZ, 6532 SZ Nijmegen, The Netherlands
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111
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Enzymatic degradation of xyloglucans by Aspergillus species: a comparative view of this genus. Appl Microbiol Biotechnol 2021; 105:2701-2711. [PMID: 33760931 DOI: 10.1007/s00253-021-11236-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 02/25/2021] [Accepted: 03/14/2021] [Indexed: 10/21/2022]
Abstract
Aspergillus species are closely associated with humanity through fermentation, infectious disease, and mycotoxin contamination of food. Members of this genus produce various enzymes to degrade plant polysaccharides, including starch, cellulose, xylan, and xyloglucan. This review focus on the machinery of the xyloglucan degradation using glycoside hydrolases, such as xyloglucanases, isoprimeverose-producing oligoxyloglucan hydrolases, and α-xylosidases, in Aspergillus species. Some xyloglucan degradation-related glycoside hydrolases are well conserved in this genus; however, other enzymes are not. Cooperative actions of these glycoside hydrolases are crucial for xyloglucan degradation in Aspergillus species. KEY POINTS: •Xyloglucan degradation-related enzymes of Aspergillus species are reviewed. •Each Aspergillus species possesses a different set of glycoside hydrolases. •The machinery of xyloglucan degradation of A. oryzae is overviewed.
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112
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Reijngoud J, Arentshorst M, Ruijmbeek C, Reid I, Alazi ED, Punt PJ, Tsang A, Ram AFJ. Loss of function of the carbon catabolite repressor CreA leads to low but inducer-independent expression from the feruloyl esterase B promoter in Aspergillus niger. Biotechnol Lett 2021; 43:1323-1336. [PMID: 33738610 PMCID: PMC8197723 DOI: 10.1007/s10529-021-03104-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 02/08/2021] [Indexed: 11/26/2022]
Abstract
Objective
With the aim to decipher the mechanisms involved in the transcriptional regulation of feruloyl esterase encoded by faeB, a genetic screen was performed to isolate A. niger mutants displaying inducer-independent expression from the faeB promoter.
Result PfaeB-amdS and PfaeB-lux dual reporter strains were constructed and used to isolate trans-acting mutants in which the expression of both reporters was increased, based on the ability to grow on acetamide plates and higher luciferase activity, respectively. The genetic screen on the non-inducing carbon source D-fructose yielded in total 111 trans-acting mutants. The genome of one of the mutants was sequenced and revealed several SNPs, including a point mutation in the creA gene encoding a transcription factor known to be involved in carbon catabolite repression. Subsequently, all mutants were analyzed for defects in carbon catabolite repression by determining sensitivity towards allyl alcohol. All except four of the 111 mutants were sensitive to allyl alcohol, indicating that the vast majority of the mutants are defective in carbon catabolite repression. The creA gene of 32 allyl alcohol sensitive mutants was sequenced and 27 of them indeed contained a mutation in the creA gene. Targeted deletion of creA in the reporter strain confirmed that the loss of CreA results in constitutive expression from the faeB promoter. Conclusion
Loss of function of CreA leads to low but inducer-independent expression from the faeB promoter in A. niger. Supplementary Information The online version contains supplementary material available at 10.1007/s10529-021-03104-2.
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Affiliation(s)
- Jos Reijngoud
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Bioscienz, Goeseelsstraat 10, 4817 MV, Breda, The Netherlands
| | - Mark Arentshorst
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Claudine Ruijmbeek
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Ian Reid
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada
| | - Ebru Demirci Alazi
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Peter J Punt
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Dutch DNA Biotech, Hugo R Kruytgebouw 4-Noord, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada
| | - Arthur F J Ram
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
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Salihu R, Abd Razak SI, Ahmad Zawawi N, Rafiq Abdul Kadir M, Izzah Ismail N, Jusoh N, Riduan Mohamad M, Hasraf Mat Nayan N. Citric acid: A green cross-linker of biomaterials for biomedical applications. Eur Polym J 2021. [DOI: 10.1016/j.eurpolymj.2021.110271] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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114
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Dong Z, Yang S, Lee BH. Bioinformatic mapping of a more precise Aspergillus niger degradome. Sci Rep 2021; 11:693. [PMID: 33436802 PMCID: PMC7804941 DOI: 10.1038/s41598-020-80028-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/15/2020] [Indexed: 11/21/2022] Open
Abstract
Aspergillus niger has the ability to produce a large variety of proteases, which are of particular importance for protein digestion, intracellular protein turnover, cell signaling, flavour development, extracellular matrix remodeling and microbial defense. However, the A. niger degradome (the full repertoire of peptidases encoded by the A. niger genome) available is not accurate and comprehensive. Herein, we have utilized annotations of A. niger proteases in AspGD, JGI, and version 12.2 MEROPS database to compile an index of at least 232 putative proteases that are distributed into the 71 families/subfamilies and 26 clans of the 6 known catalytic classes, which represents ~ 1.64% of the 14,165 putative A. niger protein content. The composition of the A. niger degradome comprises ~ 7.3% aspartic, ~ 2.2% glutamic, ~ 6.0% threonine, ~ 17.7% cysteine, ~ 31.0% serine, and ~ 35.8% metallopeptidases. One hundred and two proteases have been reassigned into the above six classes, while the active sites and/or metal-binding residues of 110 proteases were recharacterized. The probable physiological functions and active site architectures of these peptidases were also investigated. This work provides a more precise overview of the complete degradome of A. niger, which will no doubt constitute a valuable resource and starting point for further experimental studies on the biochemical characterization and physiological roles of these proteases.
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Affiliation(s)
- Zixing Dong
- Henan Provincial Engineering Laboratory of Insect Bio-Reactor and Henan Key Laboratory of Ecological Security for Water Region of Mid-Line of South-To-North, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, People's Republic of China.
| | - Shuangshuang Yang
- College of Physical Education, Nanyang Normal University, Nanyang, 473061, People's Republic of China
| | - Byong H Lee
- Department of Microbiology/Immunology, McGill University, Montreal, QC, Canada
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115
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Ellena V, Sauer M, Steiger MG. The fungal sexual revolution continues: discovery of sexual development in members of the genus Aspergillus and its consequences. Fungal Biol Biotechnol 2020; 7:17. [PMID: 33357234 PMCID: PMC7761153 DOI: 10.1186/s40694-020-00107-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/15/2020] [Indexed: 12/24/2022] Open
Abstract
Asexuality was considered to be a common feature of a large part of fungi, including those of the genus Aspergillus. However, recent advances and the available genomic and genetic engineering technologies allowed to gather more and more indications of a hidden sexuality in fungi previously considered asexual. In parallel, the acquired knowledge of the most suitable conditions for crossings was shown to be crucial to effectively promote sexual reproduction in the laboratory. These discoveries not only have consequences on our knowledge of the biological processes ongoing in nature, questioning if truly asexual fungal species exist, but they also have important implications on other research areas. For instance, the presence of sexuality in certain fungi can have effects on their pathogenicity or on shaping the ecosystem that they normally colonize. For these reasons, further investigations of the sexual potential of Aspergillus species, such as the industrially important A. niger, will be carried on.
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Affiliation(s)
- Valeria Ellena
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 18, Vienna, Austria. .,Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.
| | - Michael Sauer
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 18, Vienna, Austria.,Institute of Microbiology and Microbial Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, Austria.,CD Laboratory for Biotechnology of Glycerol, Muthgasse 18, Vienna, Austria
| | - Matthias G Steiger
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 18, Vienna, Austria.,Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
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116
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Ferrara M, Gallo A, Perrone G, Magistà D, Baker SE. Comparative Genomic Analysis of Ochratoxin A Biosynthetic Cluster in Producing Fungi: New Evidence of a Cyclase Gene Involvement. Front Microbiol 2020; 11:581309. [PMID: 33391201 PMCID: PMC7775548 DOI: 10.3389/fmicb.2020.581309] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/30/2020] [Indexed: 12/13/2022] Open
Abstract
The widespread use of Next-Generation Sequencing has opened a new era in the study of biological systems by significantly increasing the catalog of fungal genomes sequences and identifying gene clusters for known secondary metabolites as well as novel cryptic ones. However, most of these clusters still need to be examined in detail to completely understand the pathway steps and the regulation of the biosynthesis of metabolites. Genome sequencing approach led to the identification of the biosynthetic genes cluster of ochratoxin A (OTA) in a number of producing fungal species. Ochratoxin A is a potent pentaketide nephrotoxin produced by Aspergillus and Penicillium species and found as widely contaminant in food, beverages and feed. The increasing availability of several new genome sequences of OTA producer species in JGI Mycocosm and/or GenBank databanks led us to analyze and update the gene cluster structure in 19 Aspergillus and 2 Penicillium OTA producing species, resulting in a well conserved organization of OTA core genes among the species. Furthermore, our comparative genome analyses evidenced the presence of an additional gene, previously undescribed, located between the polyketide and non-ribosomal synthase genes in the cluster of all the species analyzed. The presence of a SnoaL cyclase domain in the sequence of this gene supports its putative role in the polyketide cyclization reaction during the initial steps of the OTA biosynthesis pathway. The phylogenetic analysis showed a clustering of OTA SnoaL domains in accordance with the phylogeny of OTA producing species at species and section levels. The characterization of this new OTA gene, its putative role and its expression evidence in three important representative producing species, are reported here for the first time.
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Affiliation(s)
- Massimo Ferrara
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Bari, Italy
| | - Antonia Gallo
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Lecce, Italy
| | - Giancarlo Perrone
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Bari, Italy
| | - Donato Magistà
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Bari, Italy
| | - Scott E Baker
- Functional and Systems Biology Group, Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.,DOE Joint Bioenergy Institute, Emeryville, CA, United States
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117
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Kraševec N, Novak M, Barat S, Skočaj M, Sepčić K, Anderluh G. Unconventional Secretion of Nigerolysins A from Aspergillus Species. Microorganisms 2020; 8:E1973. [PMID: 33322461 PMCID: PMC7763983 DOI: 10.3390/microorganisms8121973] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/04/2020] [Accepted: 12/09/2020] [Indexed: 01/05/2023] Open
Abstract
Aegerolysins are small lipid-binding proteins particularly abundant in fungi. Aegerolysins from oyster mushrooms interact with an insect-specific membrane lipid and, together with MACPF proteins produced by the same organism, form pesticidal pore-forming complexes. The specific interaction with the same membrane lipid was recently demonstrated for nigerolysin A2 (NigA2), an aegerolysin from Aspergillus niger. In Aspergillus species, the aegerolysins were frequently found as secreted proteins, indicating their function in fungal defense. Using immunocytochemistry and live-cell imaging we investigated the subcellular localization of the nigerolysins A in A. niger, while their secretion was addressed by secretion prediction and Western blotting. We show that both nigerolysins A are leaderless proteins that reach the cell exterior by an unconventional protein secretion. NigA proteins are evenly distributed in the cytoplasm of fungal hyphae. A detailed bioinformatics analysis of Aspergillus aegerolysins suggests that the same function occurs only in a limited number of aegerolysins. From alignment, analysis of chromosomal loci, orthology, synteny, and phylogeny it follows that the same or a similar function described for pairs of pesticidal proteins of Pleurotus sp. can be expected in species of the subgenus Circumdati, section Nigri, series Nigri, and some other species with adjacent pairs of putative pesticidal proteins.
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Affiliation(s)
- Nada Kraševec
- National Institute of Chemistry, SI-1000 Ljubljana, Slovenia; (S.B.); (G.A.)
| | - Maruša Novak
- Department of Biology, Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (M.N.); (M.S.); (K.S.)
| | - Simona Barat
- National Institute of Chemistry, SI-1000 Ljubljana, Slovenia; (S.B.); (G.A.)
- Department of Biology, Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (M.N.); (M.S.); (K.S.)
| | - Matej Skočaj
- Department of Biology, Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (M.N.); (M.S.); (K.S.)
| | - Kristina Sepčić
- Department of Biology, Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (M.N.); (M.S.); (K.S.)
| | - Gregor Anderluh
- National Institute of Chemistry, SI-1000 Ljubljana, Slovenia; (S.B.); (G.A.)
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118
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Fang Q, Du M, Chen J, Liu T, Zheng Y, Liao Z, Zhong Q, Wang L, Fang X, Wang J. Degradation and Detoxification of Aflatoxin B1 by Tea-Derived Aspergillus niger RAF106. Toxins (Basel) 2020; 12:toxins12120777. [PMID: 33291337 PMCID: PMC7762301 DOI: 10.3390/toxins12120777] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 12/02/2020] [Indexed: 11/16/2022] Open
Abstract
Microbial degradation is an effective and attractive method for eliminating aflatoxin B1 (AFB1), which is severely toxic to humans and animals. In this study, Aspergillus niger RAF106 could effectively degrade AFB1 when cultivated in Sabouraud dextrose broth (SDB) with contents of AFB1 ranging from 0.1 to 4 μg/mL. Treatment with yeast extract as a nitrogen source stimulated the degradation, but treatment with NaNO3 and NaNO2 as nitrogen sources and lactose and sucrose as carbon sources suppressed the degradation. Moreover, A. niger RAF106 still degraded AFB1 at initial pH values that ranged from 4 to 10 and at cultivation temperatures that ranged from 25 to 45 °C. In addition, intracellular enzymes or proteins with excellent thermotolerance were verified as being able to degrade AFB1 into metabolites with low or no mutagenicity. Furthermore, genomic sequence analysis indicated that the fungus was considered to be safe owing to the absence of virulence genes and the gene clusters for the synthesis of mycotoxins. These results indicate that A. niger RAF106 and its intracellular enzymes or proteins have a promising potential to be applied commercially in the processing and industry of food and feed to detoxify AFB1.
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Affiliation(s)
- Qian’an Fang
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; (Q.F.); (M.D.); (J.C.); (T.L.); (Y.Z.); (Z.L.); (Q.Z.); (L.W.)
| | - Minru Du
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; (Q.F.); (M.D.); (J.C.); (T.L.); (Y.Z.); (Z.L.); (Q.Z.); (L.W.)
| | - Jianwen Chen
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; (Q.F.); (M.D.); (J.C.); (T.L.); (Y.Z.); (Z.L.); (Q.Z.); (L.W.)
| | - Tong Liu
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; (Q.F.); (M.D.); (J.C.); (T.L.); (Y.Z.); (Z.L.); (Q.Z.); (L.W.)
| | - Yong Zheng
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; (Q.F.); (M.D.); (J.C.); (T.L.); (Y.Z.); (Z.L.); (Q.Z.); (L.W.)
| | - Zhenlin Liao
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; (Q.F.); (M.D.); (J.C.); (T.L.); (Y.Z.); (Z.L.); (Q.Z.); (L.W.)
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou 510642, China
| | - Qingping Zhong
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; (Q.F.); (M.D.); (J.C.); (T.L.); (Y.Z.); (Z.L.); (Q.Z.); (L.W.)
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou 510642, China
| | - Li Wang
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; (Q.F.); (M.D.); (J.C.); (T.L.); (Y.Z.); (Z.L.); (Q.Z.); (L.W.)
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou 510642, China
| | - Xiang Fang
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; (Q.F.); (M.D.); (J.C.); (T.L.); (Y.Z.); (Z.L.); (Q.Z.); (L.W.)
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou 510642, China
- Correspondence: (X.F.); (J.W.)
| | - Jie Wang
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; (Q.F.); (M.D.); (J.C.); (T.L.); (Y.Z.); (Z.L.); (Q.Z.); (L.W.)
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou 510642, China
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
- Correspondence: (X.F.); (J.W.)
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119
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van Leeuwe TM, Arentshorst M, Forn-Cuní G, Geoffrion N, Tsang A, Delvigne F, Meijer AH, Ram AFJ, Punt PJ. Deletion of the Aspergillus niger Pro-Protein Processing Protease Gene kexB Results in a pH-Dependent Morphological Transition during Submerged Cultivations and Increases Cell Wall Chitin Content. Microorganisms 2020; 8:E1918. [PMID: 33276589 PMCID: PMC7761569 DOI: 10.3390/microorganisms8121918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 11/30/2020] [Accepted: 11/30/2020] [Indexed: 11/23/2022] Open
Abstract
There is a growing interest in the use of post-fermentation mycelial waste to obtain cell wall chitin as an added-value product. In the pursuit to identify suitable production strains that can be used for post-fermentation cell wall harvesting, we turned to an Aspergillus niger strain in which the kexB gene was deleted. Previous work has shown that the deletion of kexB causes hyper-branching and thicker cell walls, traits that may be beneficial for the reduction in fermentation viscosity and lysis. Hyper-branching of ∆kexB was previously found to be pH-dependent on solid medium at pH 6.0, but was absent at pH 5.0. This phenotype was reported to be less pronounced during submerged growth. Here, we show a series of controlled batch cultivations at a pH range of 5, 5.5, and 6 to examine the pellet phenotype of ΔkexB in liquid medium. Morphological analysis showed that ΔkexB formed wild type-like pellets at pH 5.0, whereas the hyper-branching ΔkexB phenotype was found at pH 6.0. The transition of phenotypic plasticity was found in cultivations at pH 5.5, seen as an intermediate phenotype. Analyzing the cell walls of ΔkexB from these controlled pH-conditions showed an increase in chitin content compared to the wild type across all three pH values. Surprisingly, the increase in chitin content was found to be irrespective of the hyper-branching morphology. Evidence for alterations in cell wall make-up are corroborated by transcriptional analysis that showed a significant cell wall stress response in addition to the upregulation of genes encoding other unrelated cell wall biosynthetic genes.
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Affiliation(s)
- Tim M. van Leeuwe
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands; (T.M.v.L.); (M.A.); (P.J.P.)
| | - Mark Arentshorst
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands; (T.M.v.L.); (M.A.); (P.J.P.)
| | - Gabriel Forn-Cuní
- Institute of Biology Leiden, Animal Sciences, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands; (G.F.-C.); (A.H.M.)
| | - Nicholas Geoffrion
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC H4B1R6, Canada; (N.G.); (A.T.)
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC H4B1R6, Canada; (N.G.); (A.T.)
| | - Frank Delvigne
- TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Avenue de la Faculté, 2B, 5030 Gembloux, Belgium;
| | - Annemarie H. Meijer
- Institute of Biology Leiden, Animal Sciences, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands; (G.F.-C.); (A.H.M.)
| | - Arthur F. J. Ram
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands; (T.M.v.L.); (M.A.); (P.J.P.)
| | - Peter J. Punt
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands; (T.M.v.L.); (M.A.); (P.J.P.)
- Dutch DNA Biotech, Hugo R Kruytgebouw 4-Noord, Padualaan 8, 3584 CH Utrecht, The Netherlands
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120
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van Leeuwe TM, Wattjes J, Niehues A, Forn-Cuní G, Geoffrion N, Mélida H, Arentshorst M, Molina A, Tsang A, Meijer AH, Moerschbacher BM, Punt PJ, Ram AF. A seven-membered cell wall related transglycosylase gene family in Aspergillus niger is relevant for cell wall integrity in cell wall mutants with reduced α-glucan or galactomannan. Cell Surf 2020; 6:100039. [PMID: 32743151 PMCID: PMC7389268 DOI: 10.1016/j.tcsw.2020.100039] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/12/2020] [Accepted: 03/17/2020] [Indexed: 11/05/2022] Open
Abstract
Chitin is an important fungal cell wall component that is cross-linked to β-glucan for structural integrity. Acquisition of chitin to glucan cross-links has previously been shown to be performed by transglycosylation enzymes in Saccharomyces cerevisiae, called Congo Red hypersensitive (Crh) enzymes. Here, we characterized the impact of deleting all seven members of the crh gene family (crhA-G) in Aspergillus niger on cell wall integrity, cell wall composition and genome-wide gene expression. In this study, we show that the seven-fold crh knockout strain shows slightly compact growth on plates, but no increased sensitivity to cell wall perturbing compounds. Additionally, we found that the cell wall composition of this knockout strain was virtually identical to that of the wild type. In congruence with these data, genome-wide expression analysis revealed very limited changes in gene expression and no signs of activation of the cell wall integrity response pathway. However, deleting the entire crh gene family in cell wall mutants that are deficient in either galactofuranose or α-glucan, mainly α-1,3-glucan, resulted in a synthetic growth defect and an increased sensitivity towards Congo Red compared to the parental strains, respectively. Altogether, these results indicate that loss of the crh gene family in A. niger does not trigger the cell wall integrity response, but does play an important role in ensuring cell wall integrity in mutant strains with reduced galactofuranose or α-glucan.
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Affiliation(s)
- Tim M. van Leeuwe
- Leiden University, Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Jasper Wattjes
- Institute for Biology and Biotechnology of Plants, University of Muenster, Schlossplatz 8, 48143 Münster, Germany
| | - Anna Niehues
- Institute for Biology and Biotechnology of Plants, University of Muenster, Schlossplatz 8, 48143 Münster, Germany
| | - Gabriel Forn-Cuní
- Leiden University, Institute of Biology Leiden, Animal Science and Health, Einsteinweg 55, 2333CC Leiden, the Netherlands
| | - Nicholas Geoffrion
- Centre for Structural and Functional Genomics, Concordia University, Quebec H4B1R6, Canada
| | - Hugo Mélida
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo-UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Mark Arentshorst
- Leiden University, Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Antonio Molina
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo-UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Quebec H4B1R6, Canada
| | - Annemarie H. Meijer
- Leiden University, Institute of Biology Leiden, Animal Science and Health, Einsteinweg 55, 2333CC Leiden, the Netherlands
| | - Bruno M. Moerschbacher
- Institute for Biology and Biotechnology of Plants, University of Muenster, Schlossplatz 8, 48143 Münster, Germany
| | - Peter J. Punt
- Leiden University, Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Sylviusweg 72, 2333 BE Leiden, the Netherlands
- Dutch DNA Biotech, Hugo R Kruytgebouw 4-Noord, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Arthur F.J. Ram
- Leiden University, Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Sylviusweg 72, 2333 BE Leiden, the Netherlands
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121
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Garnham CP, Butler SG, Telmer PG, Black FE, Renaud JB, Sumarah MW. Identification and Characterization of an Aspergillus niger Amine Oxidase that Detoxifies Intact Fumonisins. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:13779-13790. [PMID: 33174732 DOI: 10.1021/acs.jafc.0c04504] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Fumonisin contamination of maize damaged by Fusarium verticillioides and related species is a major problem when it is grown under warm and dry conditions. Consumption of fumonisin contaminated food and feed is harmful to both humans and livestock. Novel tools for reducing or eliminating fumonisin toxicity may be useful to the agri-feed sector to deal with this worldwide problem. Enzymes capable of catabolizing fumonisins have been identified from microorganisms that utilize fumonisins as an energy source. However, fumonisin detoxifying enzymes produced by the very species that biosynthesize the toxin have yet to be reported. Here we describe the identification and characterization of a novel amine oxidase synthesized by the fumonisin-producing fungus Aspergillus niger. We have recombinantly expressed this A. niger enzyme in E. coli and demonstrated its ability to oxidatively deaminate intact fumonisins without requiring exogenous cofactors. This enzyme, termed AnFAO (A. niger fumonisin amine oxidase), displays robust fumonisin deamination activity across a broad range of conditions, has a high native melting temperature, and can be purified to >95% homogeneity at high yield in a one-step enrichment. AnFAO is a promising tool to remediate fumonisin-contaminated feed including maize destined for ethanol production.
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Affiliation(s)
- Christopher P Garnham
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford St, London, Ontario N5V 4T3, Canada
| | - Shane G Butler
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford St, London, Ontario N5V 4T3, Canada
| | - Patrick G Telmer
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford St, London, Ontario N5V 4T3, Canada
| | - Friday E Black
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford St, London, Ontario N5V 4T3, Canada
| | - Justin B Renaud
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford St, London, Ontario N5V 4T3, Canada
| | - Mark W Sumarah
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford St, London, Ontario N5V 4T3, Canada
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122
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Chen J, Li Z, Cheng Y, Gao C, Guo L, Wang T, Xu J. Sphinganine-Analog Mycotoxins (SAMs): Chemical Structures, Bioactivities, and Genetic Controls. J Fungi (Basel) 2020; 6:E312. [PMID: 33255427 PMCID: PMC7711896 DOI: 10.3390/jof6040312] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/20/2020] [Accepted: 11/22/2020] [Indexed: 12/20/2022] Open
Abstract
Sphinganine-analog mycotoxins (SAMs) including fumonisins and A. alternata f. sp. Lycopersici (AAL) toxins are a group of related mycotoxins produced by plant pathogenic fungi in the Fusarium genus and in Alternaria alternata f. sp. Lycopersici, respectively. SAMs have shown diverse cytotoxicity and phytotoxicity, causing adverse impacts on plants, animals, and humans, and are a destructive force to crop production worldwide. This review summarizes the structural diversity of SAMs and encapsulates the relationships between their structures and biological activities. The toxicity of SAMs on plants and animals is mainly attributed to their inhibitory activity against the ceramide biosynthesis enzyme, influencing the sphingolipid metabolism and causing programmed cell death. We also reviewed the detoxification methods against SAMs and how plants develop resistance to SAMs. Genetic and evolutionary analyses revealed that the FUM (fumonisins biosynthetic) gene cluster was responsible for fumonisin biosynthesis in Fusarium spp. Sequence comparisons among species within the genus Fusarium suggested that mutations and multiple horizontal gene transfers involving the FUM gene cluster were responsible for the interspecific difference in fumonisin synthesis. We finish by describing methods for monitoring and quantifying SAMs in food and agricultural products.
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Affiliation(s)
- Jia Chen
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (J.C.); (Z.L.); (Y.C.); (C.G.); (L.G.); (T.W.)
| | - Zhimin Li
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (J.C.); (Z.L.); (Y.C.); (C.G.); (L.G.); (T.W.)
| | - Yi Cheng
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (J.C.); (Z.L.); (Y.C.); (C.G.); (L.G.); (T.W.)
| | - Chunsheng Gao
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (J.C.); (Z.L.); (Y.C.); (C.G.); (L.G.); (T.W.)
| | - Litao Guo
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (J.C.); (Z.L.); (Y.C.); (C.G.); (L.G.); (T.W.)
| | - Tuhong Wang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (J.C.); (Z.L.); (Y.C.); (C.G.); (L.G.); (T.W.)
| | - Jianping Xu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (J.C.); (Z.L.); (Y.C.); (C.G.); (L.G.); (T.W.)
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
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Molecular analysis of Aspergillus section Nigri isolated from onion samples reveals the prevalence of A. welwitschiae. Braz J Microbiol 2020; 52:387-392. [PMID: 33094470 DOI: 10.1007/s42770-020-00390-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/16/2020] [Indexed: 10/23/2022] Open
Abstract
The aim of this study was to isolate Aspergillus section Nigri from onion samples bought in supermarkets and to analyze the fungal isolates by means of molecular data in order to differentiate A. niger and A. welwitschiae species from the other non-toxigenic species of black aspergilli, and detect genes involved in the biosynthesis of ochratoxin A and fumonisin B2. Aspergillus section Nigri were found in 98% (94/96) of the onion samples. Based on the results of multiplex PCR (performed on 500 randomly selected strains), 97.4% of the Aspergillus section Nigri strains were recognized as A. niger/A. welwitschiae. Around half of them were subjected to partial sequencing of the CaM gene to distinguish one from the other. A total of 97.9% of the isolates were identified as A. welwitschiae and only 2.1% as A. niger. The fum8 gene, involved in fumonisin B2 biosynthesis, was found in 36% of A. welwitschiae isolates, but radH and pks genes, involved in ochratoxin A biosynthesis, were found in only 2.8%. The presence/absence of fum8 gene in the A. welwitschiae genome is closely associated with ability/inability of the isolates to produce fumonisin in vitro. Based on these results, we suggest that in-depth studies are conducted to investigate the presence of fumonisins in onion bulbs.
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Wang X, Peng J, Sun L, Bonito G, Guo Y, Li Y, Fu Y. Genome Sequencing of Paecilomyces Penicillatus Provides Insights into Its Phylogenetic Placement and Mycoparasitism Mechanisms on Morel Mushrooms. Pathogens 2020; 9:pathogens9100834. [PMID: 33065983 PMCID: PMC7650745 DOI: 10.3390/pathogens9100834] [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: 09/03/2020] [Revised: 10/05/2020] [Accepted: 10/09/2020] [Indexed: 12/17/2022] Open
Abstract
Morels (Morchella spp.) are popular edible fungi with significant economic and scientific value. However, white mold disease, caused by Paecilomyces penicillatus, can reduce morel yield by up to 80% in the main cultivation area in China. Paecilomyces is a polyphyletic genus and the exact phylogenetic placement of P. penicillatus is currently still unclear. Here, we obtained the first high-quality genome sequence of P. penicillatus generated through the single-molecule real-time (SMRT) sequencing platform. The assembled draft genome of P. penicillatus was 40.2 Mb, had an N50 value of 2.6 Mb and encoded 9454 genes. Phylogenetic analysis of single-copy orthologous genes revealed that P. penicillatus is in Hypocreales and closely related to Hypocreaceae, which includes several genera exhibiting a mycoparasitic lifestyle. CAZymes analysis demonstrated that P. penicillatus encodes a large number of fungal cell wall degradation enzymes. We identified many gene clusters involved in the production of secondary metabolites known to exhibit antifungal, antibacterial, or insecticidal activities. We further demonstrated through dual culture assays that P. penicillatus secretes certain soluble compounds that are inhibitory to the mycelial growth of Morchella sextelata. This study provides insights into the correct phylogenetic placement of P. penicillatus and the molecular mechanisms that underlie P. penicillatus pathogenesis.
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Affiliation(s)
- Xinxin Wang
- Department of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China;
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (L.S.); (Y.L.)
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48842, USA; (J.P.); (G.B.)
| | - Jingyu Peng
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48842, USA; (J.P.); (G.B.)
| | - Lei Sun
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (L.S.); (Y.L.)
| | - Gregory Bonito
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48842, USA; (J.P.); (G.B.)
| | - Yuxiu Guo
- Life Science College, Northeast Normal University, Changchun 130118, China;
| | - Yu Li
- Department of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China;
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (L.S.); (Y.L.)
| | - Yongping Fu
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (L.S.); (Y.L.)
- Correspondence:
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125
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Two New Aspergillus flavus Reference Genomes Reveal a Large Insertion Potentially Contributing to Isolate Stress Tolerance and Aflatoxin Production. G3-GENES GENOMES GENETICS 2020; 10:3515-3531. [PMID: 32817124 PMCID: PMC7534430 DOI: 10.1534/g3.120.401405] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Efforts in genome sequencing in the Aspergillus genus have led to the development of quality reference genomes for several important species including A. nidulans, A. fumigatus, and A. oryzae However, less progress has been made for A. flavus As part of the effort of the USDA-ARS Annual Aflatoxin Workshop Fungal Genome Project, the isolate NRRL3357 was sequenced and resulted in a scaffold-level genome released in 2005. Our goal has been biologically driven, focusing on two areas: isolate variation in aflatoxin production and drought stress exacerbating aflatoxin production by A. flavus Therefore, we developed two reference pseudomolecule genome assemblies derived from chromosome arms for two isolates: AF13, a MAT1-2, highly stress tolerant, and highly aflatoxigenic isolate; and NRRL3357, a MAT1-1, less stress tolerant, and moderate aflatoxin producer in comparison to AF13. Here, we report these two reference-grade assemblies for these isolates through a combination of PacBio long-read sequencing and optical mapping, and coupled them with comparative, functional, and phylogenetic analyses. This analysis resulted in the identification of 153 and 45 unique genes in AF13 and NRRL3357, respectively. We also confirmed the presence of a unique 310 Kb insertion in AF13 containing 60 genes. Analysis of this insertion revealed the presence of a bZIP transcription factor, named atfC, which may contribute to isolate pathogenicity and stress tolerance. Phylogenomic analyses comparing these and other available assemblies also suggest that the species complex of A. flavus is polyphyletic.
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126
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Li C, Zhou J, Du G, Chen J, Takahashi S, Liu S. Developing Aspergillus niger as a cell factory for food enzyme production. Biotechnol Adv 2020; 44:107630. [PMID: 32919011 DOI: 10.1016/j.biotechadv.2020.107630] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 09/05/2020] [Accepted: 09/05/2020] [Indexed: 02/06/2023]
Abstract
Aspergillus niger has become one of the most important hosts for food enzyme production due to its unique food safety characteristics and excellent protein secretion systems. A series of food enzymes such as glucoamylase have been commercially produced by A. niger strains, making this species a suitable platform for the engineered of strains with improved enzyme production. However, difficulties in genetic manipulations and shortage of expression strategies limit the progress in this regard. Moreover, several mycotoxins have recently been detected in some A. niger strains, which raises the necessity for a regulatory approval process for food enzyme production. With robust strains, processing engineering strategies are also needed for producing the enzymes on a large scale, which is also challenging for A. niger, since its culture is aerobic, and non-Newtonian fluid properties are developed during submerged culture, making mixing and aeration very energy-intensive. In this article, the progress and challenges of developing A. niger for the production of food enzymes are reviewed, including its genetic manipulations, strategies for more efficient production of food enzymes, and elimination of mycotoxins for product safety.
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Affiliation(s)
- Cen Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Guocheng Du
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Jian Chen
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Shunji Takahashi
- Natural Product Biosynthesis Research Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Song Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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127
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Identification of an intracellular β-glucosidase in Aspergillus niger with transglycosylation activity. Appl Microbiol Biotechnol 2020; 104:8367-8380. [DOI: 10.1007/s00253-020-10840-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 07/29/2020] [Accepted: 08/14/2020] [Indexed: 10/23/2022]
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Zeuner B, Thomsen TB, Stringer MA, Krogh KBRM, Meyer AS, Holck J. Comparative Characterization of Aspergillus Pectin Lyases by Discriminative Substrate Degradation Profiling. Front Bioeng Biotechnol 2020; 8:873. [PMID: 32850731 PMCID: PMC7406575 DOI: 10.3389/fbioe.2020.00873] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 07/07/2020] [Indexed: 11/13/2022] Open
Abstract
Fungal genomes often contain several copies of genes that encode carbohydrate active enzymes having similar activity. The copies usually have slight sequence variability, and it has been suggested that the multigenecity represents distinct reaction optima versions of the enzyme. Whether the copies represent differences in substrate attack proficiencies of the enzyme have rarely been considered. The genomes of Aspergillus species encode several pectin lyases (EC 4.2.2.10), which all belong to polysaccharide lyase subfamily PL1_4 in the CAZy database. The enzymes differ in terms of sequence identity and phylogeny, and exhibit structural differences near the active site in their homology models. These enzymes catalyze pectin degradation via eliminative cleavage of the α-(1,4) glycosidic linkages in homogalacturonan with a preference for linkages between methyl-esterified galacturonate residues. This study examines four different pectin lyases (PelB, PelC, PelD, and PelF) encoded by the same Aspergillus sp. (namely A. luchuensis), and further compares two PelA pectin lyases from two related Aspergillus spp. (A. aculeatus and A. tubingensis). We report the phylogeny, enzyme kinetics, and enzymatic degradation profiles of the enzymes' action on apple pectin, citrus pectin, and sugar beet pectin. All the pectin lyases exerted highest reaction rate on apple pectin [degree of methoxylation (DM) 69%, degree of acetylation (DAc) 2%] and lowest reaction rate on sugar beet pectin (DM 56%, DAc 19%). Activity comparison at pH 5-5.5 produced the following ranking: PelB > PelA > PelD > PelF > PelC. The evolution of homogalacturonan-oligomer product profiles during reaction was analyzed by liquid chromatography with mass spectrometry (LC-MS) detection. This analyses revealed subtle differences in the product profiles indicating distinct substrate degradation preferences amongst the enzymes, notably with regard to acetyl substitutions. The LC-MS product profiling analysis thus disclosed that the multigenecity appears to provide the fungus with additional substrate degradation versatility. This product profiling furthermore represents a novel approach to functionally compare pectin-degrading enzymes, which can help explain structure-function relations and reaction properties of disparate copies of carbohydrate active enzymes. A better understanding of the product profiles generated by pectin modifying enzymes has significant implications for targeted pectin modification in food and biorefinery processes.
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Affiliation(s)
- Birgitte Zeuner
- Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Thore Bach Thomsen
- Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | | | - Anne S Meyer
- Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Jesper Holck
- Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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129
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Takagi S, Kojima K, Ohashi S. Proteomic analysis on Aspergillus strains that are useful for industrial enzyme production. Biosci Biotechnol Biochem 2020; 84:2241-2252. [PMID: 32693695 DOI: 10.1080/09168451.2020.1794784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A simple intracellular proteomic study was conducted to investigate the biological activities of Aspergillus niger during industrial enzyme production. A strain actively secreting a heterologous enzyme was compared to a reference strain. In total, 1824 spots on 2-D gels were analyzed using MALDI-TOF MS, yielding 343 proteins. The elevated levels of UPR components, BipA, PDI, and calnexin, and proteins related to ERAD and ROS reduction, were observed in the enzyme-producer. The results suggest the occurrence of these responses in the enzyme-producers. Major glycolytic enzymes, Fba1, EnoA, and GpdA, were abundant but at a reduced level relative to the reference, indicating a potential repression of the glycolytic pathway. Interestingly, it was observed that a portion of over-expressed heterologous enzyme accumulated inside the cells and digested during fermentation, suggesting the secretion capacity of the strain was not enough for completing secretion. Newly identified conserved-proteins, likely in signal transduction, and other proteins were also investigated. Abbreviations: 2-D: two-dimensional; UPR: unfolded protein response; ER: endoplasmic reticulum; ERAD: ER-associated protein degradation; PDI: protein disulfide-isomerase; ROS: reactive oxygen species; RESS: Repression under Secretion Stress; CSAP: Conserved Small Abundant Protein; TCTP: translationally controlled tumor protein.
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Affiliation(s)
| | | | - Shinichi Ohashi
- Genome Biotechnology Laboratory, Kanazawa-Institute of Technology , Ishikawa, Japan
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130
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Ma Y, Ling TJ, Su XQ, Jiang B, Nian B, Chen LJ, Liu ML, Zhang ZY, Wang DP, Mu YY, Jiao WW, Liu QT, Pan YH, Zhao M. Integrated proteomics and metabolomics analysis of tea leaves fermented by Aspergillus niger, Aspergillus tamarii and Aspergillus fumigatus. Food Chem 2020; 334:127560. [PMID: 32711271 DOI: 10.1016/j.foodchem.2020.127560] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 06/22/2020] [Accepted: 07/09/2020] [Indexed: 12/11/2022]
Abstract
Post-fermented Pu-erh tea (PFPT) is a microbially-fermented tea with distinct sensory qualities and multiple health benefits. Aspergillus are the dominant fungi in the fermentation and the main contributors to the characteristics of PFPT, so their underlying functions warrant detailed study. Here, tea leaves were fermented by Aspergillus niger, Aspergillus tamarii and Aspergillus fumigatus, and resulting samples (designated as Asn, Ast and Asf, respectively) were analyzed by proteomic and metabolomic methods. Changes to the composition of flavonoids, glycerophospholipids, organo-oxygen compounds and fatty acids resulting from Aspergillus fermentation were observed. Carbohydrate-active enzymes, e.g., endoglucanases and cellulases, for degradation of cellulose, starch, lignin, pectin, xylan and xyloglucan were identified. Glycoside hydrolase, glycosyltransferases, tannase, laccases, vanillyl-alcohol oxidases and benzoquinone reductase were identified and hypothesized to catalyze hydrolysis, oxidation, polymerization and degradation of phenolic compounds. Together, functions of Aspergillius were demonstrated as production of enzymes to change concentrations and compositions of metabolites in tea leaves.
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Affiliation(s)
- Yan Ma
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Tie-Jun Ling
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036 Anhui, China
| | - Xiao-Qin Su
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming, Yunnan 650201, China; Hangzhou Tea Research Institute, CHINA COOP, Hangzhou 310016, China
| | - Bin Jiang
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Bo Nian
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Li-Jiao Chen
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Ming-Li Liu
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Zheng-Yan Zhang
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Dao-Ping Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yong-Ying Mu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wen-Wen Jiao
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Qian-Ting Liu
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Ying-Hong Pan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Ming Zhao
- College of Longrun Pu-erh Tea, Yunnan Agricultural University, Kunming, Yunnan 650201, China; State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan 650201, China; The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, Yunnan 650201, China.
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131
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Steenwyk JL, Lind AL, Ries LNA, Dos Reis TF, Silva LP, Almeida F, Bastos RW, Fraga da Silva TFDC, Bonato VLD, Pessoni AM, Rodrigues F, Raja HA, Knowles SL, Oberlies NH, Lagrou K, Goldman GH, Rokas A. Pathogenic Allodiploid Hybrids of Aspergillus Fungi. Curr Biol 2020; 30:2495-2507.e7. [PMID: 32502407 PMCID: PMC7343619 DOI: 10.1016/j.cub.2020.04.071] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 02/25/2020] [Accepted: 04/24/2020] [Indexed: 12/12/2022]
Abstract
Interspecific hybridization substantially alters genotypes and phenotypes and can give rise to new lineages. Hybrid isolates that differ from their parental species in infection-relevant traits have been observed in several human-pathogenic yeasts and plant-pathogenic filamentous fungi but have yet to be found in human-pathogenic filamentous fungi. We discovered 6 clinical isolates from patients with aspergillosis originally identified as Aspergillus nidulans (section Nidulantes) that are actually allodiploid hybrids formed by the fusion of Aspergillus spinulosporus with an unknown close relative of Aspergillus quadrilineatus, both in section Nidulantes. Evolutionary genomic analyses revealed that these isolates belong to Aspergillus latus, an allodiploid hybrid species. Characterization of diverse infection-relevant traits further showed that A. latus hybrid isolates are genomically and phenotypically heterogeneous but also differ from A. nidulans, A. spinulosporus, and A. quadrilineatus. These results suggest that allodiploid hybridization contributes to the genomic and phenotypic diversity of filamentous fungal pathogens of humans.
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Affiliation(s)
- Jacob L Steenwyk
- Department of Biological Sciences, Vanderbilt University, 465 21st Avenue South, Nashville, TN 37235, USA
| | - Abigail L Lind
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, 1211 Medical Center Drive, Nashville, TN 37232, USA; Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158, USA
| | - Laure N A Ries
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo (FMRP-USP), Avenida Bandeirantes 3900, Vila Monte Alegre, 14049-900 Ribeirão Preto, São Paulo, Brazil; Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Ciências Farmacêuticas, Universidade de São Paulo, Avenida do Café S/N, Ribeirão Preto 14040-903, Brazil
| | - Thaila F Dos Reis
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo (FMRP-USP), Avenida Bandeirantes 3900, Vila Monte Alegre, 14049-900 Ribeirão Preto, São Paulo, Brazil; Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Ciências Farmacêuticas, Universidade de São Paulo, Avenida do Café S/N, Ribeirão Preto 14040-903, Brazil
| | - Lilian P Silva
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Ciências Farmacêuticas, Universidade de São Paulo, Avenida do Café S/N, Ribeirão Preto 14040-903, Brazil
| | - Fausto Almeida
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo (FMRP-USP), Avenida Bandeirantes 3900, Vila Monte Alegre, 14049-900 Ribeirão Preto, São Paulo, Brazil
| | - Rafael W Bastos
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Ciências Farmacêuticas, Universidade de São Paulo, Avenida do Café S/N, Ribeirão Preto 14040-903, Brazil
| | - Thais Fernanda de Campos Fraga da Silva
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo (FMRP-USP), Avenida Bandeirantes 3900, Vila Monte Alegre, 14049-900 Ribeirão Preto, São Paulo, Brazil
| | - Vania L D Bonato
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo (FMRP-USP), Avenida Bandeirantes 3900, Vila Monte Alegre, 14049-900 Ribeirão Preto, São Paulo, Brazil
| | - André Moreira Pessoni
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo (FMRP-USP), Avenida Bandeirantes 3900, Vila Monte Alegre, 14049-900 Ribeirão Preto, São Paulo, Brazil
| | - Fernando Rodrigues
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4715-495 Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, 4715-495 Braga, Portugal
| | - Huzefa A Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, 1400 Spring Garden Street, Greensboro, NC 27412, USA
| | - Sonja L Knowles
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, 1400 Spring Garden Street, Greensboro, NC 27412, USA
| | - Nicholas H Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, 1400 Spring Garden Street, Greensboro, NC 27412, USA
| | - Katrien Lagrou
- Department of Microbiology, Immunology and Transplantation, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; Department of Laboratory Medicine and National Reference Centre for Mycosis, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Gustavo H Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Ciências Farmacêuticas, Universidade de São Paulo, Avenida do Café S/N, Ribeirão Preto 14040-903, Brazil.
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, 465 21st Avenue South, Nashville, TN 37235, USA; Department of Biomedical Informatics, Vanderbilt University School of Medicine, 1211 Medical Center Drive, Nashville, TN 37232, USA.
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132
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Song P, Cheng L, Tian K, Zhang M, Mchunu NP, Niu D, Singh S, Prior B, Wang ZX. Biochemical characterization of two new Aspergillus niger aspartic proteases. 3 Biotech 2020; 10:303. [PMID: 32566441 DOI: 10.1007/s13205-020-02292-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/07/2020] [Indexed: 01/19/2023] Open
Abstract
Two new aspartic proteases, PepAb and PepAc (encoded by pepAb and pepAc), were heterologously expressed and biochemically characterized from Aspergillus niger F0215. They possessed a typical structure of pepsin-type aspartic protease with the conserved active residues D (84, 115), Y (131, 168) and D (281, 326), while their identity in amino acid sequences was only 19.0%. PepAb had maximum activity at pH 2.5 and 50 °C and PepAc at 3.0 and 50 °C. The specific activities of PepAb and PepAc toward casein were 1368.1 and 2081.4 U/mg, respectively. Their activities were significantly promoted by Cu2+ and Mn2+ and completely inhibited by pepstatin. PepAb exhibited higher catalytic efficiency (k cat/K m) toward soy protein isolates than casein, while PepAc showed higher catalytic efficiency toward casein. The hydrolysis capacities of PepAb and PepAc on soy protein isolates were slightly lower than that of previously identified A. niger aspartic protease, PepA (aspergillopepsin I), while the resultant peptide profiles were remarkably different for all three proteases.
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Affiliation(s)
- Peng Song
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 China
- Department of Biological Chemical Engineering, College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin, 300457 China
| | - Lei Cheng
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 China
- Department of Biological Chemical Engineering, College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin, 300457 China
| | - Kangming Tian
- Department of Biological Chemical Engineering, College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin, 300457 China
| | - Meng Zhang
- Department of Biological Chemical Engineering, College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin, 300457 China
| | - Nokuthula Peace Mchunu
- Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort, 0110 South Africa
| | - Dandan Niu
- Department of Biological Chemical Engineering, College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin, 300457 China
| | - Suren Singh
- Department of Biotechnology and Food Technology, Faculty of Applied Sciences, Durban University of Technology, P. O. Box 1334, Durban, 4001 South Africa
| | - Bernard Prior
- Department of Microbiology, University of Stellenbosch, Private Bag X1, Matieland, 7602 South Africa
| | - Zheng-Xiang Wang
- Department of Biological Chemical Engineering, College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin, 300457 China
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133
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Cheng JT, Cao F, Chen XA, Li YQ, Mao XM. Genomic and transcriptomic survey of an endophytic fungus Calcarisporium arbuscula NRRL 3705 and potential overview of its secondary metabolites. BMC Genomics 2020; 21:424. [PMID: 32580753 PMCID: PMC7315530 DOI: 10.1186/s12864-020-06813-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 06/09/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Secondary metabolites as natural products from endophytic fungi are important sources of pharmaceuticals. However, there is currently little understanding of endophytic fungi at the omics levels about their potential in secondary metabolites. Calcarisporium arbuscula, an endophytic fungus from the fruit bodies of Russulaceae, produces a variety of secondary metabolites with anti-cancer, anti-nematode and antibiotic activities. A comprehensive survey of the genome and transcriptome of this endophytic fungus will help to understand its capacity to biosynthesize secondary metabolites and will lay the foundation for the development of this precious resource. RESULTS In this study, we reported the high-quality genome sequence of C. arbuscula NRRL 3705 based on Single Molecule Real-Time sequencing technology. The genome of this fungus is over 45 Mb in size, larger than other typical filamentous fungi, and comprises 10,001 predicted genes, encoding at least 762 secretory-proteins, 386 carbohydrate-active enzymes and 177 P450 enzymes. 398 virulence factors and 228 genes related to pathogen-host interactions were also predicted in this fungus. Moreover, 65 secondary metabolite biosynthetic gene clusters were revealed, including the gene cluster for the mycotoxin aurovertins. In addition, several gene clusters were predicted to produce mycotoxins, including aflatoxin, alternariol, destruxin, citrinin and isoflavipucine. Notably, two independent gene clusters were shown that are potentially involved in the biosynthesis of alternariol. Furthermore, RNA-Seq assays showed that only expression of the aurovertin gene cluster is much stronger than expression of the housekeeping genes under laboratory conditions, consistent with the observation that aurovertins are the predominant metabolites. Gene expression of the remaining 64 gene clusters for compound backbone biosynthesis was all lower than expression of the housekeeping genes, which partially explained poor production of other secondary metabolites in this fungus. CONCLUSIONS Our omics data, along with bioinformatics analysis, indicated that C. arbuscula NRRL 3705 contains a large number of biosynthetic gene clusters and has a huge potential to produce a profound number of secondary metabolites. This work also provides the basis for development of endophytic fungi as a new resource of natural products with promising biological activities.
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Affiliation(s)
- Jin-Tao Cheng
- Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
| | - Fei Cao
- Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
| | - Xin-Ai Chen
- Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, 310058, China.,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
| | - Yong-Quan Li
- Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, 310058, China. .,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China.
| | - Xu-Ming Mao
- Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, 310058, China. .,Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China.
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134
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Díaz GV, Coniglio RO, Alvarenga AE, Zapata PD, Villalba LL, Fonseca MI. Secretomic analysis of cheap enzymatic cocktails of Aspergillus niger LBM 134 grown on cassava bagasse and sugarcane bagasse. Mycologia 2020; 112:663-676. [PMID: 32574526 DOI: 10.1080/00275514.2020.1763707] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Currently, agroindustrial wastes are little used for generating value-added products; hence, their use of these waste to produce enzymatic cocktails for the conversion of lignocellulosic biomass to fermentable sugars is a very interesting alternative in the second-generation bioethanol process. The Ascomycota fungus Aspergillus niger LBM 134 produces hydrolytic enzymes in large proportions. In this work, A. niger LBM 134 was grown on sugarcane and cassava bagasses under optimized conditions. To identify the extracellular enzymes involved in the degradation of these agroindustrial wastes, the secretomes of the culture supernatants of the fungus were analyzed and validated by biochemical assays of the enzymatic activities. A. niger LBM 134 secreted higher quantities of xylanases and accessory hemicellulases when it grew on sugarcane bagasse, whereas more cellulases, amylases, and pectinases were secreted when it grew on cassava bagasse. These findings suggest two promising enzyme cocktails for the hydrolysis of lignocellulose carbohydrate polymers to fermentable sugars. These bioinformatic analysis were functional validates through enzymatic biochemical assays that confirm the biotechnological potential of A. niger LBM 134 for the bioconversion of hemicellulosic substrates such as sugarcane and cassava bagasses.
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Affiliation(s)
- Gabriela Verónica Díaz
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones "María Ebe Reca" CONICET, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones , Ruta 12 km 7.5, C.P. 3300, Posadas, Argentina
| | - Romina Olga Coniglio
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones "María Ebe Reca" CONICET, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones , Ruta 12 km 7.5, C.P. 3300, Posadas, Argentina
| | - Adriana Elizabet Alvarenga
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones "María Ebe Reca" CONICET, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones , Ruta 12 km 7.5, C.P. 3300, Posadas, Argentina
| | - Pedro Darío Zapata
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones "María Ebe Reca" CONICET, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones , Ruta 12 km 7.5, C.P. 3300, Posadas, Argentina
| | - Laura Lidia Villalba
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones "María Ebe Reca" CONICET, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones , Ruta 12 km 7.5, C.P. 3300, Posadas, Argentina
| | - María Isabel Fonseca
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones "María Ebe Reca" CONICET, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones , Ruta 12 km 7.5, C.P. 3300, Posadas, Argentina
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135
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Jørgensen TR, Burggraaf AM, Arentshorst M, Schutze T, Lamers G, Niu J, Kwon MJ, Park J, Frisvad JC, Nielsen KF, Meyer V, van den Hondel CA, Dyer PS, Ram AF. Identification of SclB, a Zn(II)2Cys6 transcription factor involved in sclerotium formation in Aspergillus niger. Fungal Genet Biol 2020; 139:103377. [DOI: 10.1016/j.fgb.2020.103377] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 02/07/2020] [Accepted: 02/14/2020] [Indexed: 10/24/2022]
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136
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Xie Z, Fong WP, Tsang PWK. Engineering and optimization of phosphate-responsive phytase expression in Pichia pastoris yeast for phytate hydrolysis. Enzyme Microb Technol 2020; 137:109533. [PMID: 32423670 DOI: 10.1016/j.enzmictec.2020.109533] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/30/2020] [Accepted: 02/06/2020] [Indexed: 10/25/2022]
Abstract
Phytate is the major storage form of phosphorus in plants. It is present in cereals and raw materials of vegetable origin used in animal and human diets. However, non-ruminant animals have little phytase activity in their guts and, therefore, cannot digest phytate. As a result, almost all dietary phytate is discharged into the environment, causing phosphorus pollution. Phytate is also considered as an "antinutrient" for its ability to form insoluble and stable complexes with metal ions, thus reducing dietary absorption of essential minerals. It is a dire need to develop sustainable approaches for environmentally-friendly utilization for this valuable and abundant natural resource. To this end, we engineered Pichia pastoris to express and secrete phytase in a "made-to-order" fashion in response to external level of inorganic phosphate (Pi). Responsiveness to external Pi level was achieved by generating a Pi-responsive promoter library using directed evolution. The resultant yeast strains were proven to liberate Pi from wheat-based meal in a simulated in vitro digestion model. These yeast-based whole cell biocatalysts may serve as platform hosts with potential applications in food processing industry and animal waste treatment.
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Affiliation(s)
- Zhenming Xie
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Wing-Ping Fong
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Paul Wai-Kei Tsang
- Technological and Higher Education Institute of Hong Kong, Hong Kong, China.
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137
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Yang H, Cai G, Lu J, Gómez Plaza E. The production and application of enzymes related to the quality of fruit wine. Crit Rev Food Sci Nutr 2020; 61:1605-1615. [PMID: 32423236 DOI: 10.1080/10408398.2020.1763251] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Grape wine is the most widely consumed fruit wine in the world. With the increasing diversification of consumers' needs, the variety of fruit wines in the market is becoming more and more abundant. Whether it is the production of grape wine or other fruit wines these processes are inseparable from the participation of enzymes. The quality of these wines is closely related to the application of enzymes in the winemaking process. Enzymes are involved in pretreatment, fermentation, filtration, flavoring, aging and storage of fruit wines. This review systematically illustrated the role of pectinase, β-glucanase, β-glucosidase, glucose oxidase, lysozyme, protease, tannase and urease in the production of wines and their current production status and also provided a theoretical basis for better application of various enzymes in the production of various fruit wines. This knowledge could be great significance to improve the quality of fruit wines and reduce the production costs in the fruit wine industry.
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Affiliation(s)
- Hua Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, P. R. China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Wuxi, P. R. China.,School of Biotechnology, Jiangnan University, Wuxi, P. R. China.,School of Food Science and Technology, University of Murcia, Murcia, Spain
| | - Guolin Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, P. R. China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Wuxi, P. R. China.,School of Biotechnology, Jiangnan University, Wuxi, P. R. China
| | - Jian Lu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, P. R. China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Wuxi, P. R. China.,School of Biotechnology, Jiangnan University, Wuxi, P. R. China
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138
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Comparative evaluation of Aspergillus niger strains for endogenous pectin-depolymerization capacity and suitability for D-galacturonic acid production. Bioprocess Biosyst Eng 2020; 43:1549-1560. [PMID: 32328731 PMCID: PMC7378126 DOI: 10.1007/s00449-020-02347-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 04/03/2020] [Indexed: 12/11/2022]
Abstract
Pectinaceous agricultural residues rich in D-galacturonic acid (D-GalA), such as sugar beet pulp, are considered as promising feedstocks for waste-to-value conversions. Aspergillus niger is known for its strong pectinolytic activity. However, while specialized strains for production of citric acid or proteins are well characterized, this is not the case for the production of pectinases. We, therefore, systematically compared the pectinolytic capabilities of six A. niger strains (ATCC 1015, ATCC 11414, NRRL 3122, CBS 513.88, NRRL 3, and N402) using controlled batch cultivations in stirred-tank bioreactors. A. niger ATCC 11414 showed the highest polygalacturonase activity, specific protein secretion, and a suitable morphology. Furthermore, D-GalA release from sugar beet pulp was 75% higher compared to the standard lab strain A. niger N402. Our study, therefore, presents a robust initial strain selection to guide future process improvement of D-GalA production from agricultural residues and identifies a high-performance base strain for further genetic optimizations.
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139
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Rojas-Sánchez U, López-Calleja AC, Millán-Chiu BE, Fernández F, Loske AM, Gómez-Lim MA. Enhancing the yield of human erythropoietin in Aspergillus niger by introns and CRISPR-Cas9. Protein Expr Purif 2020; 168:105570. [DOI: 10.1016/j.pep.2020.105570] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/12/2020] [Accepted: 01/13/2020] [Indexed: 12/14/2022]
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140
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Zhang L, Zheng X, Cairns TC, Zhang Z, Wang D, Zheng P, Sun J. Disruption or reduced expression of the orotidine-5'-decarboxylase gene pyrG increases citric acid production: a new discovery during recyclable genome editing in Aspergillus niger. Microb Cell Fact 2020; 19:76. [PMID: 32209089 PMCID: PMC7092557 DOI: 10.1186/s12934-020-01334-z] [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: 01/08/2020] [Accepted: 03/16/2020] [Indexed: 11/15/2022] Open
Abstract
Background Aspergillus niger is a filamentous fungus used for the majority of global citric acid production. Recent developments in genome editing now enable biotechnologists to engineer and optimize A. niger. Currently, however, genetic-leads for maximizing citric acid titers in industrial A. niger isolates is limited. Results In this study, we try to engineer two citric acid A. niger production isolates, WT-D and D353, to serve as platform strains for future high-throughput genome engineering. Consequently, we used genome editing to simultaneously disrupt genes encoding the orotidine-5′-decarboxylase (pyrG) and non-homologous end-joining component (kusA) to enable use of the pyrG selection/counter selection system, and to elevate homologous recombination rates, respectively. During routine screening of these pyrG mutant strains, we unexpectedly observed a 2.17-fold increase in citric acid production when compared to the progenitor controls, indicating that inhibition of uridine/pyrimidine synthesis may increase citric acid titers. In order to further test this hypothesis, the pyrG gene was placed under the control of a tetracycline titratable cassette, which confirmed that reduced expression of this gene elevated citric acid titers in both shake flask and bioreactor fermentation. Subsequently, we conducted intracellular metabolomics analysis, which demonstrated that pyrG disruption enhanced the glycolysis flux and significantly improved abundance of citrate and its precursors. Conclusions In this study, we deliver two citric acid producing isolates which are amenable to high throughput genetic manipulation due to pyrG/kusA deletion. Strikingly, we demonstrate for the first time that A. niger pyrG is a promising genetic lead for generating citric acid hyper-producing strains. Our data support the hypothesis that uridine/pyrimidine biosynthetic pathway offer future avenues for strain engineering efforts.![]()
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Affiliation(s)
- Lihui Zhang
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Xiaomei Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Timothy C Cairns
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Zhidan Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Depei Wang
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China.
| | - Ping Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jibin Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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141
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Perez R, Luccioni M, Kamakaka R, Clamons S, Gaut N, Stirling F, Adamala KP, Silver PA, Endy D. Enabling community-based metrology for wood-degrading fungi. Fungal Biol Biotechnol 2020; 7:2. [PMID: 32206323 PMCID: PMC7081594 DOI: 10.1186/s40694-020-00092-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 02/25/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Lignocellulosic biomass could support a greatly-expanded bioeconomy. Current strategies for using biomass typically rely on single-cell organisms and extensive ancillary equipment to produce precursors for downstream manufacturing processes. Alternative forms of bioproduction based on solid-state fermentation and wood-degrading fungi could enable more direct means of manufacture. However, basic methods for cultivating wood-degrading fungi are often ad hoc and not readily reproducible. Here, we developed standard reference strains, substrates, measurements, and methods sufficient to begin to enable reliable reuse of mycological materials and products in simple laboratory settings. RESULTS We show that a widely-available and globally-regularized consumer product (Pringles™) can support the growth of wood-degrading fungi, and that growth on Pringles™-broth can be correlated with growth on media made from a fully-traceable and compositionally characterized substrate (National Institute of Standards and Technology Reference Material 8492 Eastern Cottonwood Whole Biomass Feedstock). We also establish a Relative Extension Unit (REU) framework that is designed to reduce variation in quantification of radial growth measurements. So enabled, we demonstrate that five laboratories were able to compare measurements of wood-fungus performance via a simple radial extension growth rate assay, and that our REU-based approach reduced variation in reported measurements by up to ~ 75%. CONCLUSIONS Reliable reuse of materials, measures, and methods is necessary to enable distributed bioproduction processes that can be adopted at all scales, from local to industrial. Our community-based measurement methods incentivize practitioners to coordinate the reuse of standard materials, methods, strains, and to share information supporting work with wood-degrading fungi.
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Affiliation(s)
- Rolando Perez
- Department of Bioengineering, Schools of Engineering and Medicine, Stanford University, Room 252, Shriram Center, 443 Via Ortega, Stanford, CA 94305 USA
| | - Marina Luccioni
- Department of Bioengineering, Schools of Engineering and Medicine, Stanford University, Room 252, Shriram Center, 443 Via Ortega, Stanford, CA 94305 USA
| | - Rohinton Kamakaka
- Department of MCD Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064 USA
| | - Samuel Clamons
- Department of Chemistry and Molecular Biophysics, California Institute of Technology, 1200 E. California Blvd, MC 138-78, Pasadena, CA 91125 USA
- Department of Control and Dynamical Systems, California Institute of Technology, 1200 E. California Blvd, MC 138-78, Pasadena, CA 91125 USA
| | - Nathaniel Gaut
- Department of Genetics, Cell Biology, and Development, College of Biological Sciences, University of Minnesota, 420 Washington Ave. SE, 5-178 MCB, Minneapolis, MN 55455 USA
| | - Finn Stirling
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Warren Alpert Building, Boston, MA 02115 USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 200 Longwood Avenue, Warren Alpert Building, Boston, MA 02115 USA
| | - Katarzyna P. Adamala
- Department of Genetics, Cell Biology, and Development, College of Biological Sciences, University of Minnesota, 420 Washington Ave. SE, 5-178 MCB, Minneapolis, MN 55455 USA
| | - Pamela A. Silver
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Warren Alpert Building, Boston, MA 02115 USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 200 Longwood Avenue, Warren Alpert Building, Boston, MA 02115 USA
| | - Drew Endy
- Department of Bioengineering, Schools of Engineering and Medicine, Stanford University, Room 252, Shriram Center, 443 Via Ortega, Stanford, CA 94305 USA
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142
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Houbraken J, Kocsubé S, Visagie C, Yilmaz N, Wang XC, Meijer M, Kraak B, Hubka V, Bensch K, Samson R, Frisvad J. Classification of Aspergillus, Penicillium, Talaromyces and related genera ( Eurotiales): An overview of families, genera, subgenera, sections, series and species. Stud Mycol 2020; 95:5-169. [PMID: 32855739 PMCID: PMC7426331 DOI: 10.1016/j.simyco.2020.05.002] [Citation(s) in RCA: 254] [Impact Index Per Article: 63.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The Eurotiales is a relatively large order of Ascomycetes with members frequently having positive and negative impact on human activities. Species within this order gain attention from various research fields such as food, indoor and medical mycology and biotechnology. In this article we give an overview of families and genera present in the Eurotiales and introduce an updated subgeneric, sectional and series classification for Aspergillus and Penicillium. Finally, a comprehensive list of accepted species in the Eurotiales is given. The classification of the Eurotiales at family and genus level is traditionally based on phenotypic characters, and this classification has since been challenged using sequence-based approaches. Here, we re-evaluated the relationships between families and genera of the Eurotiales using a nine-gene sequence dataset. Based on this analysis, the new family Penicillaginaceae is introduced and four known families are accepted: Aspergillaceae, Elaphomycetaceae, Thermoascaceae and Trichocomaceae. The Eurotiales includes 28 genera: 15 genera are accommodated in the Aspergillaceae (Aspergillago, Aspergillus, Evansstolkia, Hamigera, Leiothecium, Monascus, Penicilliopsis, Penicillium, Phialomyces, Pseudohamigera, Pseudopenicillium, Sclerocleista, Warcupiella, Xerochrysium and Xeromyces), eight in the Trichocomaceae (Acidotalaromyces, Ascospirella, Dendrosphaera, Rasamsonia, Sagenomella, Talaromyces, Thermomyces, Trichocoma), two in the Thermoascaceae (Paecilomyces, Thermoascus) and one in the Penicillaginaceae (Penicillago). The classification of the Elaphomycetaceae was not part of this study, but according to literature two genera are present in this family (Elaphomyces and Pseudotulostoma). The use of an infrageneric classification system has a long tradition in Aspergillus and Penicillium. Most recent taxonomic studies focused on the sectional level, resulting in a well-established sectional classification in these genera. In contrast, a series classification in Aspergillus and Penicillium is often outdated or lacking, but is still relevant, e.g., the allocation of a species to a series can be highly predictive in what functional characters the species might have and might be useful when using a phenotype-based identification. The majority of the series in Aspergillus and Penicillium are invalidly described and here we introduce a new series classification. Using a phylogenetic approach, often supported by phenotypic, physiologic and/or extrolite data, Aspergillus is subdivided in six subgenera, 27 sections (five new) and 75 series (73 new, one new combination), and Penicillium in two subgenera, 32 sections (seven new) and 89 series (57 new, six new combinations). Correct identification of species belonging to the Eurotiales is difficult, but crucial, as the species name is the linking pin to information. Lists of accepted species are a helpful aid for researchers to obtain a correct identification using the current taxonomic schemes. In the most recent list from 2014, 339 Aspergillus, 354 Penicillium and 88 Talaromyces species were accepted. These numbers increased significantly, and the current list includes 446 Aspergillus (32 % increase), 483 Penicillium (36 % increase) and 171 Talaromyces (94 % increase) species, showing the large diversity and high interest in these genera. We expanded this list with all genera and species belonging to the Eurotiales (except those belonging to Elaphomycetaceae). The list includes 1 187 species, distributed over 27 genera, and contains MycoBank numbers, collection numbers of type and ex-type cultures, subgenus, section and series classification data, information on the mode of reproduction, and GenBank accession numbers of ITS, beta-tubulin (BenA), calmodulin (CaM) and RNA polymerase II second largest subunit (RPB2) gene sequences.
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Key Words
- Acidotalaromyces Houbraken, Frisvad & Samson
- Acidotalaromyces lignorum (Stolk) Houbraken, Frisvad & Samson
- Ascospirella Houbraken, Frisvad & Samson
- Ascospirella lutea (Zukal) Houbraken, Frisvad & Samson
- Aspergillus chaetosartoryae Hubka, Kocsubé & Houbraken
- Classification
- Evansstolkia Houbraken, Frisvad & Samson
- Evansstolkia leycettana (H.C. Evans & Stolk) Houbraken, Frisvad & Samson
- Hamigera brevicompacta (H.Z. Kong) Houbraken, Frisvad & Samson
- Infrageneric classification
- New combinations, series
- New combinations, species
- New genera
- New names
- New sections
- New series
- New taxa
- Nomenclature
- Paecilomyces lagunculariae (C. Ram) Houbraken, Frisvad & Samson
- Penicillaginaceae Houbraken, Frisvad & Samson
- Penicillago kabunica (Baghd.) Houbraken, Frisvad & Samson
- Penicillago mirabilis (Beliakova & Milko) Houbraken, Frisvad & Samson
- Penicillago moldavica (Milko & Beliakova) Houbraken, Frisvad & Samson
- Phialomyces arenicola (Chalab.) Houbraken, Frisvad & Samson
- Phialomyces humicoloides (Bills & Heredia) Houbraken, Frisvad & Samson
- Phylogeny
- Polythetic classes
- Pseudohamigera Houbraken, Frisvad & Samson
- Pseudohamigera striata (Raper & Fennell) Houbraken, Frisvad & Samson
- Talaromyces resinae (Z.T. Qi & H.Z. Kong) Houbraken & X.C. Wang
- Talaromyces striatoconidius Houbraken, Frisvad & Samson
- Taxonomic novelties: New family
- Thermoascus verrucosus (Samson & Tansey) Houbraken, Frisvad & Samson
- Thermoascus yaguchii Houbraken, Frisvad & Samson
- in Aspergillus: sect. Bispori S.W. Peterson, Varga, Frisvad, Samson ex Houbraken
- in Aspergillus: ser. Acidohumorum Houbraken & Frisvad
- in Aspergillus: ser. Inflati (Stolk & Samson) Houbraken & Frisvad
- in Penicillium: sect. Alfrediorum Houbraken & Frisvad
- in Penicillium: ser. Adametziorum Houbraken & Frisvad
- in Penicillium: ser. Alutacea (Pitt) Houbraken & Frisvad
- sect. Crypta Houbraken & Frisvad
- sect. Eremophila Houbraken & Frisvad
- sect. Formosana Houbraken & Frisvad
- sect. Griseola Houbraken & Frisvad
- sect. Inusitata Houbraken & Frisvad
- sect. Lasseniorum Houbraken & Frisvad
- sect. Polypaecilum Houbraken & Frisvad
- sect. Raperorum S.W. Peterson, Varga, Frisvad, Samson ex Houbraken
- sect. Silvatici S.W. Peterson, Varga, Frisvad, Samson ex Houbraken
- sect. Vargarum Houbraken & Frisvad
- ser. Alliacei Houbraken & Frisvad
- ser. Ambigui Houbraken & Frisvad
- ser. Angustiporcata Houbraken & Frisvad
- ser. Arxiorum Houbraken & Frisvad
- ser. Atramentosa Houbraken & Frisvad
- ser. Aurantiobrunnei Houbraken & Frisvad
- ser. Avenacei Houbraken & Frisvad
- ser. Bertholletiarum Houbraken & Frisvad
- ser. Biplani Houbraken & Frisvad
- ser. Brevicompacta Houbraken & Frisvad
- ser. Brevipedes Houbraken & Frisvad
- ser. Brunneouniseriati Houbraken & Frisvad
- ser. Buchwaldiorum Houbraken & Frisvad
- ser. Calidousti Houbraken & Frisvad
- ser. Canini Houbraken & Frisvad
- ser. Carbonarii Houbraken & Frisvad
- ser. Cavernicolarum Houbraken & Frisvad
- ser. Cervini Houbraken & Frisvad
- ser. Chevalierorum Houbraken & Frisvad
- ser. Cinnamopurpurea Houbraken & Frisvad
- ser. Circumdati Houbraken & Frisvad
- ser. Clavigera Houbraken & Frisvad
- ser. Conjuncti Houbraken & Frisvad
- ser. Copticolarum Houbraken & Frisvad
- ser. Coremiiformes Houbraken & Frisvad
- ser. Corylophila Houbraken & Frisvad
- ser. Costaricensia Houbraken & Frisvad
- ser. Cremei Houbraken & Frisvad
- ser. Crustacea (Pitt) Houbraken & Frisvad
- ser. Dalearum Houbraken & Frisvad
- ser. Deflecti Houbraken & Frisvad
- ser. Egyptiaci Houbraken & Frisvad
- ser. Erubescentia (Pitt) Houbraken & Frisvad
- ser. Estinogena Houbraken & Frisvad
- ser. Euglauca Houbraken & Frisvad
- ser. Fennelliarum Houbraken & Frisvad
- ser. Flavi Houbraken & Frisvad
- ser. Flavipedes Houbraken & Frisvad
- ser. Fortuita Houbraken & Frisvad
- ser. Fumigati Houbraken & Frisvad
- ser. Funiculosi Houbraken & Frisvad
- ser. Gallaica Houbraken & Frisvad
- ser. Georgiensia Houbraken & Frisvad
- ser. Goetziorum Houbraken & Frisvad
- ser. Gracilenta Houbraken & Frisvad
- ser. Halophilici Houbraken & Frisvad
- ser. Herqueorum Houbraken & Frisvad
- ser. Heteromorphi Houbraken & Frisvad
- ser. Hoeksiorum Houbraken & Frisvad
- ser. Homomorphi Houbraken & Frisvad
- ser. Idahoensia Houbraken & Frisvad
- ser. Implicati Houbraken & Frisvad
- ser. Improvisa Houbraken & Frisvad
- ser. Indica Houbraken & Frisvad
- ser. Japonici Houbraken & Frisvad
- ser. Jiangxiensia Houbraken & Frisvad
- ser. Kalimarum Houbraken & Frisvad
- ser. Kiamaensia Houbraken & Frisvad
- ser. Kitamyces Houbraken & Frisvad
- ser. Lapidosa (Pitt) Houbraken & Frisvad
- ser. Leporum Houbraken & Frisvad
- ser. Leucocarpi Houbraken & Frisvad
- ser. Livida Houbraken & Frisvad
- ser. Longicatenata Houbraken & Frisvad
- ser. Macrosclerotiorum Houbraken & Frisvad
- ser. Monodiorum Houbraken & Frisvad
- ser. Multicolores Houbraken & Frisvad
- ser. Neoglabri Houbraken & Frisvad
- ser. Neonivei Houbraken & Frisvad
- ser. Nidulantes Houbraken & Frisvad
- ser. Nigri Houbraken & Frisvad
- ser. Nivei Houbraken & Frisvad
- ser. Nodula Houbraken & Frisvad
- ser. Nomiarum Houbraken & Frisvad
- ser. Noonimiarum Houbraken & Frisvad
- ser. Ochraceorosei Houbraken & Frisvad
- ser. Olivimuriarum Houbraken & Frisvad
- ser. Osmophila Houbraken & Frisvad
- ser. Paradoxa Houbraken & Frisvad
- ser. Paxillorum Houbraken & Frisvad
- ser. Penicillioides Houbraken & Frisvad
- ser. Phoenicea Houbraken & Frisvad
- ser. Pinetorum (Pitt) Houbraken & Frisvad
- ser. Polypaecilum Houbraken & Frisvad
- ser. Pulvini Houbraken & Frisvad
- ser. Quercetorum Houbraken & Frisvad
- ser. Raistrickiorum Houbraken & Frisvad
- ser. Ramigena Houbraken & Frisvad
- ser. Restricti Houbraken & Frisvad
- ser. Robsamsonia Houbraken & Frisvad
- ser. Rolfsiorum Houbraken & Frisvad
- ser. Roseopurpurea Houbraken & Frisvad
- ser. Rubri Houbraken & Frisvad
- ser. Salinarum Houbraken & Frisvad
- ser. Samsoniorum Houbraken & Frisvad
- ser. Saturniformia Houbraken & Frisvad
- ser. Scabrosa Houbraken & Frisvad
- ser. Sclerotigena Houbraken & Frisvad
- ser. Sclerotiorum Houbraken & Frisvad
- ser. Sheariorum Houbraken & Frisvad
- ser. Simplicissima Houbraken & Frisvad
- ser. Soppiorum Houbraken & Frisvad
- ser. Sparsi Houbraken & Frisvad
- ser. Spathulati Houbraken & Frisvad
- ser. Spelaei Houbraken & Frisvad
- ser. Speluncei Houbraken & Frisvad
- ser. Spinulosa Houbraken & Frisvad
- ser. Stellati Houbraken & Frisvad
- ser. Steyniorum Houbraken & Frisvad
- ser. Sublectatica Houbraken & Frisvad
- ser. Sumatraensia Houbraken & Frisvad
- ser. Tamarindosolorum Houbraken & Frisvad
- ser. Teporium Houbraken & Frisvad
- ser. Terrei Houbraken & Frisvad
- ser. Thermomutati Houbraken & Frisvad
- ser. Thiersiorum Houbraken & Frisvad
- ser. Thomiorum Houbraken & Frisvad
- ser. Unguium Houbraken & Frisvad
- ser. Unilaterales Houbraken & Frisvad
- ser. Usti Houbraken & Frisvad
- ser. Verhageniorum Houbraken & Frisvad
- ser. Versicolores Houbraken & Frisvad
- ser. Virgata Houbraken & Frisvad
- ser. Viridinutantes Houbraken & Frisvad
- ser. Vitricolarum Houbraken & Frisvad
- ser. Wentiorum Houbraken & Frisvad
- ser. Westlingiorum Houbraken & Frisvad
- ser. Whitfieldiorum Houbraken & Frisvad
- ser. Xerophili Houbraken & Frisvad
- series Tularensia (Pitt) Houbraken & Frisvad
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Affiliation(s)
- J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - S. Kocsubé
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - C.M. Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - N. Yilmaz
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - X.-C. Wang
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 3, 1st Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - M. Meijer
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - B. Kraak
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - V. Hubka
- Department of Botany, Charles University in Prague, Prague, Czech Republic
| | - K. Bensch
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - R.A. Samson
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - J.C. Frisvad
- Department of Biotechnology and Biomedicine Technical University of Denmark, Søltofts Plads, B. 221, Kongens Lyngby, DK 2800, Denmark
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143
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Daly P, Peng M, Mitchell HD, Kim Y, Ansong C, Brewer H, de Gijsel P, Lipton MS, Markillie LM, Nicora CD, Orr G, Wiebenga A, Hildén KS, Kabel MA, Baker SE, Mäkelä MR, de Vries RP. Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation. Environ Microbiol 2020; 22:1154-1166. [PMID: 31876091 PMCID: PMC7065180 DOI: 10.1111/1462-2920.14907] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/20/2019] [Indexed: 11/27/2022]
Abstract
Saprobic fungi, such as Aspergillus niger, grow as colonies consisting of a network of branching and fusing hyphae that are often considered to be relatively uniform entities in which nutrients can freely move through the hyphae. In nature, different parts of a colony are often exposed to different nutrients. We have investigated, using a multi-omics approach, adaptation of A. niger colonies to spatially separated and compositionally different plant biomass substrates. This demonstrated a high level of intra-colony differentiation, which closely matched the locally available substrate. The part of the colony exposed to pectin-rich sugar beet pulp and to xylan-rich wheat bran showed high pectinolytic and high xylanolytic transcript and protein levels respectively. This study therefore exemplifies the high ability of fungal colonies to differentiate and adapt to local conditions, ensuring efficient use of the available nutrients, rather than maintaining a uniform physiology throughout the colony.
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Affiliation(s)
- Paul Daly
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8, 3584 CT UtrechtThe Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8, 3584 CT UtrechtThe Netherlands
| | - Hugh D. Mitchell
- Biological Sciences DivisionsPacific Northwest National LaboratoryRichlandWA99352USA
| | - Young‐Mo Kim
- Biological Sciences DivisionsPacific Northwest National LaboratoryRichlandWA99352USA
| | - Charles Ansong
- Biological Sciences DivisionsPacific Northwest National LaboratoryRichlandWA99352USA
| | - Heather Brewer
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWA99352USA
| | - Peter de Gijsel
- Laboratory of Food ChemistryWageningen UniversityBornse Weilanden 9, 6708 WG WageningenThe Netherlands
| | - Mary S. Lipton
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWA99352USA
| | - Lye Meng Markillie
- Biological Sciences DivisionsPacific Northwest National LaboratoryRichlandWA99352USA
| | - Carrie D. Nicora
- Biological Sciences DivisionsPacific Northwest National LaboratoryRichlandWA99352USA
| | - Galya Orr
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWA99352USA
| | - Ad Wiebenga
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8, 3584 CT UtrechtThe Netherlands
| | - Kristiina S. Hildén
- Department of MicrobiologyUniversity of HelsinkiViikinkaari 9, 00790 HelsinkiFinland
| | - Mirjam A. Kabel
- Laboratory of Food ChemistryWageningen UniversityBornse Weilanden 9, 6708 WG WageningenThe Netherlands
| | - Scott E. Baker
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWA99352USA
| | - Miia R. Mäkelä
- Department of MicrobiologyUniversity of HelsinkiViikinkaari 9, 00790 HelsinkiFinland
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular PhysiologyUtrecht UniversityUppsalalaan 8, 3584 CT UtrechtThe Netherlands
- Department of MicrobiologyUniversity of HelsinkiViikinkaari 9, 00790 HelsinkiFinland
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144
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Ferrara M, Logrieco AF, Moretti A, Susca A. A loop-mediated isothermal amplification (LAMP) assay for rapid detection of fumonisin producing Aspergillus species. Food Microbiol 2020; 90:103469. [PMID: 32336366 DOI: 10.1016/j.fm.2020.103469] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/11/2019] [Accepted: 02/19/2020] [Indexed: 11/25/2022]
Abstract
Fumonisins contamination of food commodities is a worldwide problem, especially for maize. The ability to produce fumonisinsis a trait of several species of Fusarium, mainly F. verticillioides and F. proliferatum on maize, and some Aspergillus species. A. niger and its sister species A. welwitschiae, can contribute to fumonisin B2 (FB2) accumulation in maize kernels, although to a lesser extent than fumonisin-producing Fusarium species. Fumonisins risk monitoring represents an effective strategy in the integrated approach for mycotoxin risk management and reduction. The availability of a user-friendlymolecular assay for the detection oftoxigenic fungal species represents a valuable tool in understanding and managing upcoming mycotoxin contamination. In this study, we developed a LAMP assay, based on the detection of fum10, for a rapid and specific molecular detection of FB2-producing A. niger and A. welwistchiae, potentially useful to perform monitoring directly "on site" in maize chain. Results showed that very low amounts of conidia are suitable to detect the presence of the target gene, thus providing information about the presence of FB2-producing Aspergillus species and the possible upcoming fumonisins contamination in maize. The assay was combined with a suitable protocol for "in field" crude DNA extraction and a colorimetric method for easy naked-eye evaluationof results, offering a reliable and user-friendly tool to support effective reduction strategies of mycotoxin contamination in crop management programs.
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Affiliation(s)
- Massimo Ferrara
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Bari, Italy.
| | - Antonio F Logrieco
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Bari, Italy
| | - Antonio Moretti
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Bari, Italy
| | - Antonia Susca
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Bari, Italy
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145
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Upton DJ, McQueen-Mason SJ, Wood AJ. In silico evolution of Aspergillus niger organic acid production suggests strategies for switching acid output. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:27. [PMID: 32123544 PMCID: PMC7038614 DOI: 10.1186/s13068-020-01678-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 02/06/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND The fungus Aspergillus niger is an important industrial organism for citric acid fermentation; one of the most efficient biotechnological processes. Previously we introduced a dynamic model that captures this process in the industrially relevant batch fermentation setting, providing a more accurate predictive platform to guide targeted engineering. In this article we exploit this dynamic modelling framework, coupled with a robust genetic algorithm for the in silico evolution of A. niger organic acid production, to provide solutions to complex evolutionary goals involving a multiplicity of targets and beyond the reach of simple Boolean gene deletions. We base this work on the latest metabolic models of the parent citric acid producing strain ATCC1015 dedicated to organic acid production with the required exhaustive genomic coverage needed to perform exploratory in silico evolution. RESULTS With the use of our informed evolutionary framework, we demonstrate targeted changes that induce a complete switch of acid output from citric to numerous different commercially valuable target organic acids including succinic acid. We highlight the key changes in flux patterns that occur in each case, suggesting potentially valuable targets for engineering. We also show that optimum acid productivity is achieved through a balance of organic acid and biomass production, requiring finely tuned flux constraints that give a growth rate optimal for productivity. CONCLUSIONS This study shows how a genome-scale metabolic model can be integrated with dynamic modelling and metaheuristic algorithms to provide solutions to complex metabolic engineering goals of industrial importance. This framework for in silico guided engineering, based on the dynamic batch growth relevant to industrial processes, offers considerable potential for future endeavours focused on the engineering of organisms to produce valuable products.
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Affiliation(s)
- Daniel J. Upton
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD UK
| | | | - A. Jamie Wood
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD UK
- Department of Mathematics, University of York, Heslington, York, YO10 5DD UK
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146
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de Vries RP, Mäkelä MR. Genomic and Postgenomic Diversity of Fungal Plant Biomass Degradation Approaches. Trends Microbiol 2020; 28:487-499. [PMID: 32396827 DOI: 10.1016/j.tim.2020.01.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/15/2019] [Accepted: 01/16/2020] [Indexed: 10/25/2022]
Abstract
Plant biomass degradation by fungi is a widely studied and applied field of science, due to its relevance for the global carbon cycle and many biotechnological applications. Before the genome era, many of the in-depth studies focused on a relatively small number of species, whereas now, many species can be addressed in detail, revealing the large variety in the approach used by fungi to degrade plant biomass. This variation is found at many levels and includes genomic adaptation to the preferred biomass component, but also different approaches to degrade this component by diverse sets of activities encoded in the genome. Even larger differences have been observed using transcriptome and proteome studies, even between closely related species, suggesting a high level of adaptation in individual species. A better understanding of the drivers of this diversity could be highly valuable in developing more efficient biotechnology approaches for the enzymatic conversion of plant biomass.
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Affiliation(s)
- Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands.
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Helsinki, Finland
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147
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Lin H, Zhao J, Zhang Q, Cui S, Fan Z, Chen H, Tian C. Identification and Characterization of a Cellodextrin Transporter in Aspergillus niger. Front Microbiol 2020; 11:145. [PMID: 32117164 PMCID: PMC7020610 DOI: 10.3389/fmicb.2020.00145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 01/21/2020] [Indexed: 11/13/2022] Open
Abstract
Aspergillus niger produces a wide spectrum of extracellular polysaccharide hydrolases that hydrolyze cellulose into soluble glucose and cellodextrins. Transporters are essential for sugar uptake, yet it is not clear whether cellodextrin transporters exist in A. niger. Here, one cellulose inducible cellodextrin transporter CtA was identified in A. niger B2. It was found that CtA not only could transport cellobiose, but also cellotriose, cellotetraose, and cellopentaose. The yeast strain YPβG-CtA, expressing cellodextrin transporter CtA and an intracellular β-glucosidase, grew on cellobiose with the cell growth rate of 0.0830 ± 0.0113 h–1 under aerobic condition. Furthermore, the engineered yeast could produce 1.1 g/L ethanol anaerobically on cellobiose in 2 days. The identification of CtA provides evidence that the cellodextrin uptake is a complementary strategy of cellulose utilization in A. niger, and the CtA could be a strong transporter candidate for constructing engineered cellodextrin-utilizing microorganisms.
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Affiliation(s)
- Hui Lin
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Jun Zhao
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Qingqing Zhang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Shixiu Cui
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Zhiliang Fan
- Department of Biological and Agricultural Engineering, University of California, Davis, Davis, CA, United States
| | - Hongge Chen
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Chaoguang Tian
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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148
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Sui YF, Ouyang LM, Schütze T, Cheng S, Meyer V, Zhuang YP. Comparative genomics of the aconidial Aspergillus niger strain LDM3 predicts genes associated with its high protein secretion capacity. Appl Microbiol Biotechnol 2020; 104:2623-2637. [DOI: 10.1007/s00253-020-10398-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/02/2020] [Accepted: 01/20/2020] [Indexed: 01/14/2023]
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149
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Dong H, Yu D, Wang B, Pan L. Identification and Characterization of a Novel Basic Helix-Loop-Helix Transcription Factor of Phospholipid Synthesis Regulation in Aspergillus niger. Front Microbiol 2020; 10:2985. [PMID: 31993030 PMCID: PMC6962311 DOI: 10.3389/fmicb.2019.02985] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 12/10/2019] [Indexed: 11/13/2022] Open
Abstract
The synthesis of phospholipids relies on a sort of genes, whose promoter regions contain inositol-sensitive upstream activation sequence (UASINO) and are regulated by the basic helix-loop-helix (bHLH)-type ino2/ino4 transcription factor (TF) pair. Ten putative bHLH TFs have been found through whole genome sequencing of Aspergillus niger, but none of these TFs have been characterized. In this study, we identified and characterized the bHLH-type TF ino2(An02g04350) in A. niger. Electrophoretic mobility shift assay (EMSA) and yeast two-hybrid assay demonstrated that ino2 functions as a homodimer in UASINO genes (e.g., ino1 and cho1) and binds to opi1(An1g02370) in vitro. Real-time quantitative PCR of ino1 and quantification of total phospholipid indicated that the ino2 disruptant downregulated the transcription of ino1 and the amount of total cellular phosphatidylinositol. In addition, phenotype analyses showed that a loss of ino2 led to resistance to cell wall interference and DNA damage. Comparative transcriptome analyses showed that more than 1000 genes and GO terms associated with UASINO, endoplasmic reticulum-associated protein degradation, phosphatidylinositol synthesis, chitin synthesis, and fatty acid synthesis were differentially expressed in Δino2 compared to the wild type (WT). Taken together, these observations indicate that the bHLH TF ino2 functions as a homodimer that regulates the synthesis of phosphatidylinositol, fatty acid, and chitin and influences the homeostasis of the endoplasmic reticulum membrane.
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Affiliation(s)
- Hongzhi Dong
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.,Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, China
| | - Dou Yu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.,Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, China
| | - Bin Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.,Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, China
| | - Li Pan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.,Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, China
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150
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Huang L, Dong L, Wang B, Pan L. The transcription factor PrtT and its target protease profiles in Aspergillus niger are negatively regulated by carbon sources. Biotechnol Lett 2020; 42:613-624. [PMID: 31970554 DOI: 10.1007/s10529-020-02806-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 01/13/2020] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To survey genome-scale protease profiles regulated by the Aspergillus niger transcription factor PrtT and further controlled by carbon sources. RESULTS The PrtT disruption mutant (delprtT) and overexpression (OEprtT) strains were successfully generated and further confirmed by phenotypic and protease activity analysis. RNA-seq analysis of WT and mutants identified 32 differentially expressed protease genes, which mostly belonged to serine-type peptidases, aspartic-type endopeptidases, aminopeptidases and carboxypeptidases. Furthermore, based on the MEME predicted motif analysis of the PrtT promoter, EMSA and phenotypic and qRT-PCR analyses confirmed that the carbon metabolism regulator AmyR directly regulated the protease genes and their regulatory factor PrtT. CONCLUSION Thirty-two PrtT-regulated protease genes were identified by RNA-seq, and the secondary carbon source regulator AmyR was found to have a negative regulatory effect on the expression of PrtT and its target protease genes.
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Affiliation(s)
- Lianggang Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, No. 382, Waihuan East Rd, Guangzhou, 510006, China
| | - Liangbo Dong
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, No. 382, Waihuan East Rd, Guangzhou, 510006, China
| | - Bin Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, No. 382, Waihuan East Rd, Guangzhou, 510006, China.,Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Li Pan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, No. 382, Waihuan East Rd, Guangzhou, 510006, China. .,Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, China.
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