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Physiology and Biotechnology of Aspergillus niger
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Physiology and Biotechnology of Aspergillus niger

A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Fungi in Agriculture and Biotechnology".

Deadline for manuscript submissions: closed (31 October 2023) | Viewed by 10001

Special Issue Editors

Dr. Sandra Garrigues

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Guest Editor
Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA-CSIC), Valencia, Spain
Interests: fungal biotechnology; fungal synthetic biology; genome editing; fungal biofactories; gene regulation; antifungals; plant biomass conversion; circular economy
Special Issues, Collections and Topics in MDPI journals
Dr. Ronnie Lubbers

E-Mail Website
Guest Editor
Molecular Microbiology and Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
Interests: bioremediation; utilization of renewable resources; carbon and nitrogen metabolism; aromatic compounds; microbial plastic degradation; lignin; pollutants
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Aspergillus niger is a filamentous ascomycete fungus well known for its ability to produce organic acids, proteins, enzymes and primary and secondary metabolites. All of these compounds have many applications in various fields, including the food and feed, pulp and paper, and textile industries. In the last century, scientists have developed A. niger as an industrial workhorse for many biotechnological applications. However, several challenges still limit the application of this fungus at the industrial level. This Special Issue is dedicated to any type of study that addresses A. niger physiology and biotechnology, from genome editing to molecular and omics studies, which aim to improve A. niger for its application at the industrial level.

We believe this Special Issue will provide an up-to-date overview and novel insights of the potential of this fungus as a workhorse for biotechnological and industrial purposes.

Dr. Sandra Garrigues
Dr. Ronnie Lubbers
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Journal of Fungi is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • fungal biofactories 
  • fungal biotechnology 
  • fungal synthetic biology 
  • genetic engineering 
  • metabolic engineering 
  • genome editing 
  • enzymes 
  • secondary metabolism

Published Papers (6 papers)

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Research

14 pages, 3123 KiB  
Article
Genome Mining Reveals a Surprising Number of Sugar Reductases in Aspergillus niger
by Astrid Mueller, Li Xu, Claudia Heine, Tila Flach, Miia R. Mäkelä and Ronald P. de Vries
J. Fungi 2023, 9(12), 1138; https://doi.org/10.3390/jof9121138 - 24 Nov 2023
Viewed by 1257
Abstract
Metabolic engineering of filamentous fungi has received increasing attention in recent years, especially in the context of creating better industrial fungal cell factories to produce a wide range of valuable enzymes and metabolites from plant biomass. Recent studies into the pentose catabolic pathway [...] Read more.
Metabolic engineering of filamentous fungi has received increasing attention in recent years, especially in the context of creating better industrial fungal cell factories to produce a wide range of valuable enzymes and metabolites from plant biomass. Recent studies into the pentose catabolic pathway (PCP) in Aspergillus niger have revealed functional redundancy in most of the pathway steps. In this study, a closer examination of the A. niger genome revealed five additional paralogs for the three original pentose reductases (LarA, XyrA, XyrB). Analysis of these genes using phylogeny, in vitro and in vivo functional analysis of the enzymes, and gene expression revealed that all can functionally replace LarA, XyrA, and XyrB. However, they are also active on several other sugars, suggesting a role for them in other pathways. This study therefore reveals the diversity of primary carbon metabolism in fungi, suggesting an intricate evolutionary process that distinguishes different species. In addition, through this study, the metabolic toolkit for synthetic biology and metabolic engineering of A. niger and other fungal cell factories has been expanded. Full article
(This article belongs to the Special Issue Physiology and Biotechnology of Aspergillus niger)
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16 pages, 5974 KiB  
Article
ChsA, a Class Ⅱ Chitin Synthase, Contributes to Asexual Conidiation, Mycelial Morphology, Cell Wall Integrity, and the Production of Enzymes and Organic Acids in Aspergillus niger
by Yunqi Zhu, Tong Liu, Yingsi Wang, Guojun Chen, Xiang Fang, Gang Zhou and Jie Wang
J. Fungi 2023, 9(8), 801; https://doi.org/10.3390/jof9080801 - 29 Jul 2023
Viewed by 1114
Abstract
Chitin synthases (CHSs) are vital enzymes for the synthesis of chitin and play important and differential roles in fungal development, cell wall integrity, environmental adaptation, virulence, and metabolism in fungi. However, except for ChsC, a class III CHS, little is known about the [...] Read more.
Chitin synthases (CHSs) are vital enzymes for the synthesis of chitin and play important and differential roles in fungal development, cell wall integrity, environmental adaptation, virulence, and metabolism in fungi. However, except for ChsC, a class III CHS, little is known about the functions of CHSs in Aspergillus niger, an important fungus that is widely applied in the fermentation industry and food processing, as well as a spoilage fungus of food and a human pathogen. This study showed the important functions of ChsA, a class II CHS, in A. niger using multi-phenotypic and transcriptional analyses under various conditions. The deletion of chsA led to severe defects in conidiation on different media and resulted in the formation of smaller and less compact pellets with less septa in hyphal cells during submerged fermentation. Compared with the WT, the ΔchsA mutants exhibited less chitin content, reduced growth under the stresses of cell wall-disturbing and oxidative agents, more released protoplasts, a thicker conidial wall, decreased production of amylases, pectinases, cellulases, and malic acid, and increased citric acid production. However, ΔchsA mutants displayed insignificant changes in their sensitivity to osmotic agents and infection ability on apple. These findings concurred with the alteration in the transcript levels and enzymatic activities of some phenotype-related genes. Conclusively, ChsA is important for cell wall integrity and mycelial morphology, and acts as a positive regulator of conidiation, cellular responses to oxidative stresses, and the production of malic acid and some enzymes, but negatively regulates the citric acid production in A. niger. Full article
(This article belongs to the Special Issue Physiology and Biotechnology of Aspergillus niger)
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17 pages, 1460 KiB  
Article
Mutations in the Second Alternative Oxidase Gene: A New Approach to Group Aspergillus niger Strains
by Michel Flipphi, Alexandra Márton, Vivien Bíró, Norbert Ág, Erzsébet Sándor, Erzsébet Fekete and Levente Karaffa
J. Fungi 2023, 9(5), 570; https://doi.org/10.3390/jof9050570 - 13 May 2023
Cited by 1 | Viewed by 1273
Abstract
Alternative oxidase is a terminal oxidase in the branched mitochondrial electron transport chain of most fungi including Aspergillus niger (subgenus Circumdati, section Nigri). A second, paralogous aox gene (aoxB) is extant in some A. niger isolates but also present in two [...] Read more.
Alternative oxidase is a terminal oxidase in the branched mitochondrial electron transport chain of most fungi including Aspergillus niger (subgenus Circumdati, section Nigri). A second, paralogous aox gene (aoxB) is extant in some A. niger isolates but also present in two divergent species of the subgenus Nidulantes—A. calidoustus and A. implicatus—as well as in Penicillium swiecickii. Black aspergilli are cosmopolitan opportunistic fungi that can cause diverse mycoses and acute aspergillosis in immunocompromised individuals. Amongst the approximately 75 genome-sequenced A. niger strains, aoxB features considerable sequence variation. Five mutations were identified that rationally affect transcription or function or terminally modify the gene product. One mutant allele that occurs in CBS 513.88 and A. niger neotype strain CBS 554.65 involves a chromosomal deletion that removes exon 1 and intron 1 from aoxB. Another aoxB allele results from retrotransposon integration. Three other alleles result from point mutations: a missense mutation of the start codon, a frameshift, and a nonsense mutation. A. niger strain ATCC 1015 has a full-length aoxB gene. The A. niger sensu stricto complex can thus be subdivided into six taxa according to extant aoxB allele, which may facilitate rapid and accurate identification of individual species Full article
(This article belongs to the Special Issue Physiology and Biotechnology of Aspergillus niger)
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16 pages, 10358 KiB  
Article
Engineering a Phosphoketolase Pathway to Supplement Cytosolic Acetyl-CoA in Aspergillus niger Enables a Significant Increase in Citric Acid Production
by Jiao Liu, Shanshan Zhang, Wenhao Li, Guanyi Wang, Zhoujie Xie, Wei Cao, Weixia Gao and Hao Liu
J. Fungi 2023, 9(5), 504; https://doi.org/10.3390/jof9050504 - 23 Apr 2023
Cited by 1 | Viewed by 1556
Abstract
Citric acid is widely used in the food, chemical and pharmaceutical industries. Aspergillus niger is the workhorse used for citric acid production in industry. A canonical citrate biosynthesis that occurred in mitochondria was well established; however, some research suggested that the cytosolic citrate [...] Read more.
Citric acid is widely used in the food, chemical and pharmaceutical industries. Aspergillus niger is the workhorse used for citric acid production in industry. A canonical citrate biosynthesis that occurred in mitochondria was well established; however, some research suggested that the cytosolic citrate biosynthesis pathway may play a role in this chemical production. Here, the roles of cytosolic phosphoketolase (PK), acetate kinase (ACK) and acetyl-CoA synthetase (ACS) in citrate biosynthesis were investigated by gene deletion and complementation in A. niger. The results indicated that PK, ACK and ACS were important for cytosolic acetyl-CoA accumulation and had significant effects on citric acid biosynthesis. Subsequently, the functions of variant PKs and phosphotransacetylase (PTA) were evaluated, and their efficiencies were determined. Finally, an efficient PK-PTA pathway was reconstructed in A. niger S469 with Ca-PK from Clostridium acetobutylicum and Ts-PTA from Thermoanaerobacterium saccharolyticum. The resultant strain showed an increase of 96.4% and 88% in the citrate titer and yield, respectively, compared with the parent strain in the bioreactor fermentation. These findings indicate that the cytosolic citrate biosynthesis pathway is important for citric acid biosynthesis, and increasing the cytosolic acetyl-CoA level can significantly enhance citric acid production. Full article
(This article belongs to the Special Issue Physiology and Biotechnology of Aspergillus niger)
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16 pages, 3158 KiB  
Article
Identification of Aspergillus niger Aquaporins Involved in Hydrogen Peroxide Signaling
by Thanaporn Laothanachareon, Enrique Asin-Garcia, Rita J. M. Volkers, Juan Antonio Tamayo-Ramos, Vitor A. P. Martins dos Santos and Peter J. Schaap
J. Fungi 2023, 9(4), 499; https://doi.org/10.3390/jof9040499 - 21 Apr 2023
Cited by 3 | Viewed by 1557
Abstract
Aspergillus niger is a robust microbial cell factory for organic acid production. However, the regulation of many industrially important pathways is still poorly understood. The regulation of the glucose oxidase (Gox) expression system, involved in the biosynthesis of gluconic acid, has recently been [...] Read more.
Aspergillus niger is a robust microbial cell factory for organic acid production. However, the regulation of many industrially important pathways is still poorly understood. The regulation of the glucose oxidase (Gox) expression system, involved in the biosynthesis of gluconic acid, has recently been uncovered. The results of that study show hydrogen peroxide, a by-product of the extracellular conversion of glucose to gluconate, has a pivotal role as a signaling molecule in the induction of this system. In this study, the facilitated diffusion of hydrogen peroxide via aquaporin water channels (AQPs) was studied. AQPs are transmembrane proteins of the major intrinsic proteins (MIPs) superfamily. In addition to water and glycerol, they may also transport small solutes such as hydrogen peroxide. The genome sequence of A. niger N402 was screened for putative AQPs. Seven AQPs were found and could be classified into three main groups. One protein (AQPA) belonged to orthodox AQP, three (AQPB, AQPD, and AQPE) were grouped in aquaglyceroporins (AQGP), two (AQPC and AQPF) were in X-intrinsic proteins (XIPs), and the other (AQPG) could not be classified. Their ability to facilitate diffusion of hydrogen peroxide was identified using yeast phenotypic growth assays and by studying AQP gene knock-outs in A. niger. The X-intrinsic protein AQPF appears to play roles in facilitating hydrogen peroxide transport across the cellular membrane in both Saccharomyces cerevisiae and A. niger experiments. Full article
(This article belongs to the Special Issue Physiology and Biotechnology of Aspergillus niger)
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14 pages, 2118 KiB  
Article
The Amylolytic Regulator AmyR of Aspergillus niger Is Involved in Sucrose and Inulin Utilization in a Culture-Condition-Dependent Manner
by Roland S. Kun, Sonia Salazar-Cerezo, Mao Peng, Yu Zhang, Emily Savage, Anna Lipzen, Vivian Ng, Igor V. Grigoriev, Ronald P. de Vries and Sandra Garrigues
J. Fungi 2023, 9(4), 438; https://doi.org/10.3390/jof9040438 - 04 Apr 2023
Cited by 1 | Viewed by 1933
Abstract
Filamentous fungi degrade complex plant material to its monomeric building blocks, which have many biotechnological applications. Transcription factors play a key role in plant biomass degradation, but little is known about their interactions in the regulation of polysaccharide degradation. Here, we deepened the [...] Read more.
Filamentous fungi degrade complex plant material to its monomeric building blocks, which have many biotechnological applications. Transcription factors play a key role in plant biomass degradation, but little is known about their interactions in the regulation of polysaccharide degradation. Here, we deepened the knowledge about the storage polysaccharide regulators AmyR and InuR in Aspergillus niger. AmyR controls starch degradation, while InuR is involved in sucrose and inulin utilization. In our study, the phenotypes of A. niger parental, ΔamyR, ΔinuR and ΔamyRΔinuR strains were assessed in both solid and liquid media containing sucrose or inulin as carbon source to evaluate the roles of AmyR and InuR and the effect of culture conditions on their functions. In correlation with previous studies, our data showed that AmyR has a minor contribution to sucrose and inulin utilization when InuR is active. In contrast, growth profiles and transcriptomic data showed that the deletion of amyR in the ΔinuR background strain resulted in more pronounced growth reduction on both substrates, mainly evidenced by data originating from solid cultures. Overall, our results show that submerged cultures do not always reflect the role of transcription factors in the natural growth condition, which is better represented on solid substrates. Importance: The type of growth has critical implications in enzyme production by filamentous fungi, a process that is controlled by transcription factors. Submerged cultures are the preferred setups in laboratory and industry and are often used for studying the physiology of fungi. In this study, we showed that the genetic response of A. niger to starch and inulin was highly affected by the culture condition, since the transcriptomic response obtained in a liquid environment did not fully match the behavior of the fungus in a solid environment. These results have direct implications in enzyme production and would help industry choose the best approaches to produce specific CAZymes for industrial purposes. Full article
(This article belongs to the Special Issue Physiology and Biotechnology of Aspergillus niger)
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