Expression-based clustering of CAZyme-encoding genes of Aspergillus niger

Co-production of sugars and aroma compounds from tobacco waste using biomass-degrading enzymes produced by Aspergillus brunneoviolaceus Ab-10

Biomass-degrading enzymes produced by microorganisms have a great potential in the processing of agricultural wastes. In order to produce suitable biomass-degrading enzymes for releasing sugars and aroma compounds from tobacco scraps, the feasibility of directly using the scraps as a carbon source for enzyme production was investigated in this study. By comparative studies of ten fungal strains isolated from tobacco leaves, Aspergillus brunneoviolaceus Ab-10 was found to produce an efficient enzyme mixture for the saccharification of tobacco scraps. Proteomic analysis identified a set of plant biomass-degrading enzymes in the enzyme mixture, including amylases, hemicellulases, cellulases and pectinases. At a substrate concentration of 100 g/L and enzyme dosage of 4 mg/g, glucose of 17.6 g/L was produced from tobacco scraps using the crude enzyme produced by A. brunneoviolaceus Ab-10. In addition, the contents of 23 volatile molecules, including the aroma compounds 4-ketoisophorone and benzyl alcohol, were significantly increased after the enzymatic treatment. The results provide a strategy for valorization of tobacco waste by integrating the production of biomass-degrading enzymes into the tobacco scrap processing system.

Insights in inulin binding and inulin oligosaccharide formation by novel multi domain endo-inulinases from Botrytis cinerea

World-wide, pathogenic fungi such as Botrytis cinerea cause tremendous yield losses in terms of food production and post-harvest food decay. Many fungi produce inulin-type oligosaccharides (IOSs) from inulin through endo-inulinases which typically show a two domain structure. B.cinerea lacks a two domain endo-inulinase but contains a three domain structure instead. Genome mining revealed three and four domain (d4) enzymes in the fungal kingdom. Here, three and two domain enzymes were compared in their capacity to produce IOSs from inulin. Hill kinetics were observed in three domain enzymes as compared to Michaelis-Menten kinetics in two domain enzymes, suggesting that the N-terminal extension functions as a carbohydrate binding module. Analysis of the IOS product profiles generated from purified GF6, GF12, GF16 and GF18 inulins and extensive sugar docking approaches led to enhanced insights in the active site functioning, revealing subtle differences between the endo-inulinases from Aspergillus niger and B. cinerea. Improved insights in structure-function relationships in fungal endo-inulinases offer opportunities to develop superior enzymes for the production of specific IOS formulations to improve plant and animal health (priming agents, prebiotics).

Genome-wide transcription landscape of citric acid producing Aspergillus niger in response to glucose gradient

Aspergillus niger is the main industrial workhorse for global citric acid production. This fungus has complex sensing and signaling pathways to respond to environmental nutrient fluctuations. As the preferred primary carbon source, glucose also acts as a critical signal to trigger intracellular bioprocesses. Currently, however, there is still a knowledge gap in systems-level understanding of metabolic and cellular responses to this vital carbon source. In this study, we determined genome-wide transcriptional changes of citric acid-producing Aspergillus niger in response to external glucose gradient. It demonstrated that external glucose fluctuation led to transcriptional reprogramming of many genes encoding proteins involved in fundamental cellular process, including ribosomal biogenesis, carbon transport and catabolism, glucose sensing and signaling. The major glucose catabolism repressor creA maintained a stable expression independent of external glucose, while creB and creD showed significant downregulation and upregulation by the glucose increase. Notably, several high-affinity glucose transporters encoding genes, including mstA, were greatly upregulated when glucose was depleted, while the expression of low-affinity glucose transporter mstC was glucose-independent, which showed clear concordance with their protein levels detected by in situ fluorescence labeling assay. In addition, we also observed that the citric acid exporter cexA was observed to be transcriptionally regulated by glucose availability, which was correlated with extracellular citric acid secretion. These discoveries not only deepen our understanding of the transcriptional regulation of glucose but also shed new light on the adaptive evolutionary mechanism of citric acid production of A. niger.

Space exposure enhanced pectin-degrading enzymes expression and activity in Aspergillus costaricaensis

Aspergillus is a well-studied fungal genus that is widely used in the processing of plant biomass in industries. This study investigated the effects of space exposure on the ability of Aspergillus costaricaensis, a filamentous fungus isolated from rotten orange peel, to degrade pectin. These fungal spores were carried into space by the Long March 5B carrier rocket and exposed to cosmic radiation for 79 h. After the flight, these spores were resuscitated, and then the growing strains were screened with pectin as the sole carbon source, and the pectinase activity was evaluated. A mutant with increased biomass accumulation ability and pectin-degrading activity compared to the ground control strain was obtained. Comparative transcriptome analysis revealed that several CAZymes genes were significantly upregulated in the mutant, especially those related to pectin degradation. Among the 44 pectinases identified from the annotated genome, 42 were up-regulated. The activities of these pectinases are able to synergistically break down the structure of pectin. In addition, the expression of some genes involved in metabolism, sugar transport, and stress response was altered. These results imply that space exposure might serve as a potential mutagenesis breeding technique, offering the opportunity to acquire biomass-degrading microbial strains with potential for industrial application.

Comparative Genomics and Transcriptomics Analyses Reveal Divergent Plant Biomass-Degrading Strategies in Fungi

Plant biomass is one of the most abundant renewable carbon sources, which holds great potential for replacing current fossil-based production of fuels and chemicals. In nature, fungi can efficiently degrade plant polysaccharides by secreting a broad range of carbohydrate-active enzymes (CAZymes), such as cellulases, hemicellulases, and pectinases. Due to the crucial role of plant biomass-degrading (PBD) CAZymes in fungal growth and related biotechnology applications, investigation of their genomic diversity and transcriptional dynamics has attracted increasing attention. In this project, we systematically compared the genome content of PBD CAZymes in six taxonomically distant species, Aspergillus niger, Aspergillus nidulans, Penicillium subrubescens, Trichoderma reesei, Phanerochaete chrysosporium, and Dichomitus squalens, as well as their transcriptome profiles during growth on nine monosaccharides. Considerable genomic variation and remarkable transcriptomic diversity of CAZymes were identified, implying the preferred carbon source of these fungi and their different methods of transcription regulation. In addition, the specific carbon utilization ability inferred from genomics and transcriptomics was compared with fungal growth profiles on corresponding sugars, to improve our understanding of the conversion process. This study enhances our understanding of genomic and transcriptomic diversity of fungal plant polysaccharide-degrading enzymes and provides new insights into designing enzyme mixtures and metabolic engineering of fungi for related industrial applications.

The Amylolytic Regulator AmyR of Aspergillus niger Is Involved in Sucrose and Inulin Utilization in a Culture-Condition-Dependent Manner

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.

Biochemical characterization of a glycoside hydrolase family 43 β-D-galactofuranosidase from the fungus Aspergillus niger

β-D-Galactofuranose (Galf) and its polysaccharides are found in bacteria, fungi and protozoa but do not occur in mammalian tissues, and thus represent a specific target for anti-pathogenic drugs. Understanding the enzymatic degradation of these polysaccharides is therefore of great interest, but the identity of fungal enzymes with exclusively galactofuranosidase activity has so far remained elusive. Here we describe the identification and characterization of a galactofuranosidase from the industrially important fungus Aspergillus niger. Analysis of glycoside hydrolase family 43 subfamily 34 (GH43_34) members via conserved unique peptide patterns and phylogeny, revealed the occurrence of distinct clusters and, by comparison with specificities of characterized bacterial members, suggested a basis for prediction of enzyme specificity. Using this rationale, in tandem with molecular docking, we identified a putative β-D-galactofuranosidase from A. niger which was recombinantly produced in Escherichia coli. The Galf-specific hydrolase, encoded by xynD demonstrates maximum activity at pH 5, 25 °C towards 4-nitrophenyl-β-galactofuranoside (pNP-β-Galf), with a K_m of 17.9 ± 1.9 mM and V_max of 70.6 ± 5.3 µM min^-1. The characterization of this first fungal GH43 galactofuranosidase offers further molecular insight into the degradation of Galf-containing structures.

Identification of an l-Arabitol Transporter from Aspergillus niger

l-arabitol is an intermediate of the pentose catabolic pathway in fungi but can also be used as a carbon source by many fungi, suggesting the presence of transporters for this polyol. In this study, an l-arabitol transporter, LatA, was identified in Aspergillus niger. Growth and expression profiles as well as sugar consumption analysis indicated that LatA only imports l-arabitol and is regulated by the arabinanolytic transcriptional activator AraR. Moreover, l-arabitol production from wheat bran was increased in a metabolically engineered A. niger mutant by the deletion of latA, indicating its potential for improving l-arabitol-producing cell factories. Phylogenetic analysis showed that homologs of LatA are widely conserved in fungi.

The Sugar Metabolic Model of Aspergillus niger Can Only Be Reliably Transferred to Fungi of Its Phylum

Fungi play a critical role in the global carbon cycle by degrading plant polysaccharides to small sugars and metabolizing them as carbon and energy sources. We mapped the well-established sugar metabolic network of Aspergillus niger to five taxonomically distant species (Aspergillus nidulans, Penicillium subrubescens, Trichoderma reesei, Phanerochaete chrysosporium and Dichomitus squalens) using an orthology-based approach. The diversity of sugar metabolism correlates well with the taxonomic distance of the fungi. The pathways are highly conserved between the three studied Eurotiomycetes (A. niger, A. nidulans, P. subrubescens). A higher level of diversity was observed between the T. reesei and A. niger, and even more so for the two Basidiomycetes. These results were confirmed by integrative analysis of transcriptome, proteome and metabolome, as well as growth profiles of the fungi growing on the corresponding sugars. In conclusion, the establishment of sugar pathway models in different fungi revealed the diversity of fungal sugar conversion and provided a valuable resource for the community, which would facilitate rational metabolic engineering of these fungi as microbial cell factories.

Detecting and identifying glycoside hydrolases using cyclophellitol-derived activity-based probes

The ability to detect active enzymes in a complex mixture of folded proteins (e.g., secretome, cell lysate) generally relies on observations of catalytic ability, necessitating the development of an activity assay that is compatible with the sample and selective for the enzyme(s) of interest. Deconvolution of the contributions of different enzymes to an observed catalytic ability further necessitates an often-challenging protein separation. The advent of broadly reactive activity-based probes (ABPs) for retaining glycoside hydrolases (GHs) has enabled an alternative, often complementary, assay for active GHs. Using activity-based protein profiling (ABPP) techniques, many retaining glycoside hydrolases can be separated, detected, and identified with high sensitivity and selectivity. This chapter outlines ABPP methods for the detection and identification of retaining glycoside hydrolases from microbial sources, including protein sample preparation from bacterial lysates and fungal secretomes, enzyme labeling and detection via fluorescence, and enzyme identification using affinity-based enrichment coupled to peptide sequencing following isobaric labeling.

Unraveling the regulation of sugar beet pulp utilization in the industrially relevant fungus Aspergillus niger

Efficient utilization of agro-industrial waste, such as sugar beet pulp, is crucial for the bio-based economy. The fungus Aspergillus niger possesses a wide array of enzymes that degrade complex plant biomass substrates, and several regulators have been reported to play a role in their production. The role of the regulators GaaR, AraR, and RhaR in sugar beet pectin degradation has previously been reported. However, genetic regulation of the degradation of sugar beet pulp has not been assessed in detail. In this study, we generated a set of single and combinatorial deletion mutants targeting the pectinolytic regulators GaaR, AraR, RhaR, and GalX as well as the (hemi-)cellulolytic regulators XlnR and ClrB to address their relative contribution to the utilization of sugar beet pulp. We show that A. niger has a flexible regulatory network, adapting to the utilization of (hemi-)cellulose at early timepoints when pectin degradation is impaired.

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Major sugar beet pulp components are sequentially utilized by A. niger

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Contribution of major regulators toward sugar beet pulp utilization was compared

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Deletion of araR and clrB showed high impact on growth after 8 and 24 h, respectively

Machine learning prediction of novel pectinolytic enzymes in Aspergillus niger through integrating heterogeneous (post-) genomics data

Pectinolytic enzymes are a variety of enzymes involved in breaking down pectin, a complex and abundant plant cell-wall polysaccharide. In nature, pectinolytic enzymes play an essential role in allowing bacteria and fungi to depolymerize and utilize pectin. In addition, pectinases have been widely applied in various industries, such as the food, wine, textile, paper and pulp industries. Due to their important biological function and increasing industrial potential, discovery of novel pectinolytic enzymes has received global interest. However, traditional enzyme characterization relies heavily on biochemical experiments, which are time consuming, laborious and expensive. To accelerate identification of novel pectinolytic enzymes, an automatic approach is needed. We developed a machine learning (ML) approach for predicting pectinases in the industrial workhorse fungus, Aspergillus niger. The prediction integrated a diverse range of features, including evolutionary profile, gene expression, transcriptional regulation and biochemical characteristics. Results on both the training and the independent testing dataset showed that our method achieved over 90 % accuracy, and recalled over 60 % of pectinolytic genes. Application of the ML model on the A. niger genome led to the identification of 83 pectinases, covering both previously described pectinases and novel pectinases that do not belong to any known pectinolytic enzyme family. Our study demonstrated the tremendous potential of ML in discovery of new industrial enzymes through integrating heterogeneous (post-) genomimcs data.

Revisiting a 'simple' fungal metabolic pathway reveals redundancy, complexity and diversity

Next to d-glucose, the pentoses l-arabinose and d-xylose are the main monosaccharide components of plant cell wall polysaccharides and are therefore of major importance in biotechnological applications that use plant biomass as a substrate. Pentose catabolism is one of the best-studied pathways of primary metabolism of Aspergillus niger, and an initial outline of this pathway with individual enzymes covering each step of the pathway has been previously established. However, although growth on l-arabinose and/or d-xylose of most pentose catabolic pathway (PCP) single deletion mutants of A. niger has been shown to be negatively affected, it was not abolished, suggesting the involvement of additional enzymes. Detailed analysis of the single deletion mutants of the known A. niger PCP genes led to the identification of additional genes involved in the pathway. These results reveal a high level of complexity and redundancy in this pathway, emphasizing the need for a comprehensive understanding of metabolic pathways before entering metabolic engineering of such pathways for the generation of more efficient fungal cell factories.

The Cultivation Method Affects the Transcriptomic Response of Aspergillus niger to Growth on Sugar Beet Pulp

In nature, filamentous fungi are exposed to diverse nutritional sources and changes in substrate availability. Conversely, in submerged cultures, mycelia are continuously exposed to the existing substrates, which are depleted over time. Submerged cultures are the preferred choice for experimental setups in laboratory and industry and are often used for understanding the physiology of fungi. However, to what extent the cultivation method affects fungal physiology, with respect to utilization of natural substrates, has not been addressed in detail. Here, we compared the transcriptomic responses of Aspergillus niger grown in submerged culture and solid culture, both containing sugar beet pulp (SBP) as a carbon source. The results showed that expression of CAZy (Carbohydrate Active enZyme)-encoding and sugar catabolic genes in liquid SBP was time dependent. Moreover, additional components of SBP delayed the A. niger response to the degradation of pectin present in SBP. In addition, we demonstrated that liquid cultures induced wider transcriptome variability than solid cultures. Although there was a correlation regarding sugar metabolic gene expression patterns between liquid and solid cultures, it decreased in the case of CAZyme-encoding genes. In conclusion, the transcriptomic response of A. niger to SBP is influenced by the culturing method, limiting the value of liquid cultures for understanding the behavior of fungi in natural habitats. IMPORTANCE Understanding the interaction between filamentous fungi and their natural and biotechnological environments has been of great interest for the scientific community. Submerged cultures are preferred over solid cultures at a laboratory scale to study the natural response of fungi to different stimuli found in nature (e.g., carbon/nitrogen sources, pH). However, whether and to what extent submerged cultures introduce variation in the physiology of fungi during growth on plant biomass have not been studied in detail. In this study, we compared the transcriptomic responses of Aspergillus niger to growth on liquid and solid cultures containing sugar beet pulp (a by-product of the sugar industry) as a carbon source. We demonstrate that the transcriptomic response of A. niger was highly affected by the culture condition, since the transcriptomic response obtained in a liquid environment could not fully explain the behavior of the fungus in a solid environment. This could partially explain the differences often observed between the phenotypes on plates compared to liquid cultures.

Blocking utilization of major plant biomass polysaccharides leads Aspergillus niger towards utilization of minor components

Fungi produce a wide range of enzymes that allow them to grow on diverse plant biomass. Wheat bran is a low-cost substrate with high potential for biotechnological applications. It mainly contains cellulose and (arabino)xylan, as well as starch, proteins, lipids and lignin to a lesser extent. In this study, we dissected the regulatory network governing wheat bran degradation in Aspergillus niger to assess the relative contribution of the regulators to the utilization of this plant biomass substrate. Deletion of genes encoding transcription factors involved in (hemi-)cellulose utilization (XlnR, AraR, ClrA and ClrB) individually and in combination significantly reduced production of polysaccharide-degrading enzymes, but retained substantial growth on wheat bran. Proteomic analysis suggested the ability of A. niger to grow on other carbon components, such as starch, which was confirmed by the additional deletion of the amylolytic regulator AmyR. Growth was further reduced but not impaired, indicating that other minor components provide sufficient energy for residual growth, displaying the flexibility of A. niger, and likely other fungi, in carbon utilization. Better understanding of the complexity and flexibility of fungal regulatory networks will facilitate the generation of more efficient fungal cell factories that use plant biomass as a substrate.

Efficient chito-oligosaccharide utilization requires two TonB-dependent transporters and one hexosaminidase in Cellvibrio japonicus

Chitin utilization by microbes plays a significant role in biosphere carbon and nitrogen cycling, and studying the microbial approaches used to degrade chitin will facilitate our understanding of bacterial strategies to degrade a broad range of recalcitrant polysaccharides. The early stages of chitin depolymerization by the bacterium Cellvibrio japonicus have been characterized and are dependent on one chitin-specific lytic polysaccharide monooxygenase and nonredundant glycoside hydrolases from the family GH18 to generate chito-oligosaccharides for entry into metabolism. Here, we describe the mechanisms for the latter stages of chitin utilization by C. japonicus with an emphasis on the fate of chito-oligosaccharides. Our systems biology approach combined transcriptomics and bacterial genetics using ecologically relevant substrates to determine the essential mechanisms for chito-oligosaccharide transport and catabolism in C. japonicus. Using RNAseq analysis we found a coordinated expression of genes that encode polysaccharide-degrading enzymes. Mutational analysis determined that the hex20B gene product, predicted to encode a hexosaminidase, was required for efficient utilization of chito-oligosaccharides. Furthermore, two gene loci (CJA_0353 and CJA_1157), which encode putative TonB-dependent transporters, were also essential for chito-oligosaccharides utilization. This study further develops our model of C. japonicus chitin metabolism and may be predictive for other environmentally or industrially important bacteria.

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

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.

Re-routing of Sugar Catabolism Provides a Better Insight Into Fungal Flexibility in Using Plant Biomass-Derived Monomers as Substrates

The filamentous ascomycete Aspergillus niger has received increasing interest as a cell factory, being able to efficiently degrade plant cell wall polysaccharides as well as having an extensive metabolism to convert the released monosaccharides into value added compounds. The pentoses D-xylose and L-arabinose are the most abundant monosaccharides in plant biomass after the hexose D-glucose, being major constituents of xylan, pectin and xyloglucan. In this study, the influence of selected pentose catabolic pathway (PCP) deletion strains on growth on plant biomass and re-routing of sugar catabolism was addressed to gain a better understanding of the flexibility of this fungus in using plant biomass-derived monomers. The transcriptome, metabolome and proteome response of three PCP mutant strains, ΔlarAΔxyrAΔxyrB, ΔladAΔxdhAΔsdhA and ΔxkiA, grown on wheat bran (WB) and sugar beet pulp (SBP), was evaluated. Our results showed that despite the absolute impact of these PCP mutations on pure pentose sugars, they are not as critical for growth of A. niger on more complex biomass substrates, such as WB and SBP. However, significant phenotypic variation was observed between the two biomass substrates, but also between the different PCP mutants. This shows that the high sugar heterogeneity of these substrates in combination with the high complexity and adaptability of the fungal sugar metabolism allow for activation of alternative strategies to support growth.

CreA-mediated repression of gene expression occurs at low monosaccharide levels during fungal plant biomass conversion in a time and substrate dependent manner

Carbon catabolite repression enables fungi to utilize the most favourable carbon source in the environment, and is mediated by a key regulator, CreA, in most fungi. CreA-mediated regulation has mainly been studied at high monosaccharide concentrations, an uncommon situation in most natural biotopes. In nature, many fungi rely on plant biomass as their major carbon source by producing enzymes to degrade plant cell wall polysaccharides into metabolizable sugars. To determine the role of CreA when fungi grow in more natural conditions and in particular with respect to degradation and conversion of plant cell walls, we compared transcriptomes of a creA deletion and reference strain of the ascomycete Aspergillus niger during growth on sugar beet pulp and wheat bran. Transcriptomics, extracellular sugar concentrations and growth profiling of A. niger on a variety of carbon sources, revealed that also under conditions with low concentrations of free monosaccharides, CreA has a major effect on gene expression in a strong time and substrate composition dependent manner. In addition, we compared the CreA regulon from five fungi during their growth on crude plant biomass or cellulose. It showed that CreA commonly regulated genes related to carbon metabolism, sugar transport and plant cell wall degrading enzymes across different species. We therefore conclude that CreA has a crucial role for fungi also in adapting to low sugar concentrations as occurring in their natural biotopes, which is supported by the presence of CreA orthologs in nearly all fungi.

Combinatorial Engineering of Transcriptional Activators in Penicillium oxalicum for Improved Production of Corn-Fiber-Degrading Enzymes

Enzymatic conversion of corn fiber to fermentable sugars is beneficial to improving the economic efficiency of corn processing. In this work, the filamentous fungus Penicillium oxalicum was found to secrete enzymes for efficient saccharification of un-pretreated corn fiber. Separate engineering of transcriptional activators ClrB, XlnR, and AraR led to enhanced production of different sets of lignocellulolytic enzymes. Particularly, the enzymes produced by XlnR- and AraR-engineered strains showed a synergistic effect in corn fiber saccharification. Combinatorial engineering of all three activators generated a strain MCAX with 3.1- to 51.0-fold increases in lignocellulolytic enzyme production compared with the parent strain. In addition, the enzymes of strain MCAX released significantly more fermentable sugars from corn fiber than those of the parent strain at the same protein dosage. The results suggest that this strain has potential for on-site production of enzymes for corn fiber saccharification.

Developing Aspergillus niger as a cell factory for food enzyme production

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.

Carbohydrate Binding Modules: Diversity of Domain Architecture in Amylases and Cellulases From Filamentous Microorganisms

Enzymatic degradation of abundant renewable polysaccharides such as cellulose and starch is a field that has the attention of both the industrial and scientific community. Most of the polysaccharide degrading enzymes are classified into several glycoside hydrolase families. They are often organized in a modular manner which includes a catalytic domain connected to one or more carbohydrate-binding modules. The carbohydrate-binding modules (CBM) have been shown to increase the proximity of the enzyme to its substrate, especially for insoluble substrates. Therefore, these modules are considered to enhance enzymatic hydrolysis. These properties have played an important role in many biotechnological applications with the aim to improve the efficiency of polysaccharide degradation. The domain organization of glycoside hydrolases (GHs) equipped with one or more CBM does vary within organisms. This review comprehensively highlights the presence of CBM as ancillary modules and explores the diversity of GHs carrying one or more of these modules that actively act either on cellulose or starch. Special emphasis is given to the cellulase and amylase distribution within the filamentous microorganisms from the genera of Streptomyces and Aspergillus that are well known to have a great capacity for secreting a wide range of these polysaccharide degrading enzyme. The potential of the CBM and other ancillary domains for the design of improved polysaccharide decomposing enzymes is discussed.

Genome Sequencing and Analysis of the Fungal Symbiont of Sirex noctilio, Amylostereum areolatum: Revealing the Biology of Fungus-Insect Mutualism

Sirex noctilio (F.), together with Amylostereum areolatum, a wood-decaying symbiotic fungus, causes severe damage to Pinus species worldwide. In China, it causes extensive death of Mongolian pine (Pinus sylvestris var. mongolica). There is an obligate dependency mutualism between the woodwasp and its fungus. Studies have suggested that the fungal growth rate affected the size of the wasps: larger adults emerged from sites with a higher fungus growth rate. This genome is the first reported genome sequence of a woodwasp symbiotic fungus. Genome sequence analysis of this fungus would prove the possibility of A. areolatum volatiles affecting the host selection of S. noctilio on a molecular basis. We further clarified that A. areolatum was a strict obligate symbiotic fungus and that it would provide S. noctilio with a suitable environment and with nutrients for the larval growth. These results would lay a foundation for our understanding of the mechanism of this entomogenous symbiosis.

Amylostereum areolatum is the symbiotic fungus of the Eurasian woodwasp, Sirex noctilio, a globally invasive species. The mutualistic symbiont is associated with the woodwasp, assisting the damage process and providing nutrition for its insect partners. Colonization and growth of A. areolatum have essential impacts on the development and spread of S. noctilio, though the mechanism of interaction between the two has been poorly described. In this study, the first genome of this symbiotic fungus was sequenced, assembled, and annotated. The assembled A. areolatum genome was 57.5 Mb (54.51% GC content) with 15,611 protein-coding genes. We identified 580 carbohydrate-active enzymes (CAZymes), 661 genes associated with pathogen-host interactions, and 318 genes encoding transport proteins in total. The genome annotation revealed 10 terpene/phytoene synthases responsible for terpenoid biosynthesis, which could be classified into three clades. Terpene synthase gene clusters in clade II were conserved well across Russulales. In this cluster, genes encoding mevalonate kinase (MK), EGR12 (COG1557), and nonplant terpene cyclases (cd00687) were the known biosynthesis and regulatory genes. Genome sequence analysis of this fungus would prove the possibility of A. areolatum volatiles affecting the host selection of S. noctilio on a molecular basis. We further clarified that A. areolatum was a strict obligate symbiotic fungus. The wasps might protect the fungus before it was introduced into a suitable host substrate by oviposition, while the fungus would provide S. noctilio with a suitable environment and nutrients for the larval growth. These results would lay a foundation for our understanding of the mechanism of this entomogenous symbiosis.

IMPORTANCESirex noctilio (F.), together with Amylostereum areolatum, a wood-decaying symbiotic fungus, causes severe damage to Pinus species worldwide. In China, it causes extensive death of Mongolian pine (Pinus sylvestris var. mongolica). There is an obligate dependency mutualism between the woodwasp and its fungus. Studies have suggested that the fungal growth rate affected the size of the wasps: larger adults emerged from sites with a higher fungus growth rate. This genome is the first reported genome sequence of a woodwasp symbiotic fungus. Genome sequence analysis of this fungus would prove the possibility of A. areolatum volatiles affecting the host selection of S. noctilio on a molecular basis. We further clarified that A. areolatum was a strict obligate symbiotic fungus and that it would provide S. noctilio with a suitable environment and with nutrients for the larval growth. These results would lay a foundation for our understanding of the mechanism of this entomogenous symbiosis.

Succession of physiological stages hallmarks the transcriptomic response of the fungus Aspergillus niger to lignocellulose

BACKGROUND

Understanding how fungi degrade lignocellulose is a cornerstone of improving renewables-based biotechnology, in particular for the production of hydrolytic enzymes. Considerable progress has been made in investigating fungal degradation during time-points where CAZyme expression peaks. However, a robust understanding of the fungal survival strategies over its life time on lignocellulose is thereby missed. Here we aimed to uncover the physiological responses of the biotechnological workhorse and enzyme producer Aspergillus niger over its life time to six substrates important for biofuel production.

RESULTS

We analysed the response of A. niger to the feedstock Miscanthus and compared it with our previous study on wheat straw, alone or in combination with hydrothermal or ionic liquid feedstock pretreatments. Conserved (substrate-independent) metabolic responses as well as those affected by pretreatment and feedstock were identified via multivariate analysis of genome-wide transcriptomics combined with targeted transcript and protein analyses and mapping to a metabolic model. Initial exposure to all substrates increased fatty acid beta-oxidation and lipid metabolism transcripts. In a strain carrying a deletion of the ortholog of the Aspergillus nidulans fatty acid beta-oxidation transcriptional regulator farA, there was a reduction in expression of selected lignocellulose degradative CAZyme-encoding genes suggesting that beta-oxidation contributes to adaptation to lignocellulose. Mannan degradation expression was wheat straw feedstock-dependent and pectin degradation was higher on the untreated substrates. In the later life stages, known and novel secondary metabolite gene clusters were activated, which are of high interest due to their potential to synthesize bioactive compounds.

CONCLUSION

In this study, which includes the first transcriptional response of Aspergilli to Miscanthus, we highlighted that life time as well as substrate composition and structure (via variations in pretreatment and feedstock) influence the fungal responses to lignocellulose. We also demonstrated that the fungal response contains physiological stages that are conserved across substrates and are typically found outside of the conditions with high CAZyme expression, as exemplified by the stages that are dominated by lipid and secondary metabolism.

Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation

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.

Genomic and Postgenomic Diversity of Fungal Plant Biomass Degradation Approaches

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.

Identification of a gene encoding the last step of the L-rhamnose catabolic pathway in Aspergillus niger revealed the inducer of the pathway regulator

In fungi, L-rhamnose (Rha) is converted via four enzymatic steps into pyruvate and L-lactaldehyde, which enter central carbon metabolism. In Aspergillus niger, only the genes involved in the first three steps of the Rha catabolic pathway have been identified and characterized, and the inducer of the pathway regulator RhaR remained unknown. In this study, we identified the gene (lkaA) involved in the conversion of L-2-keto-3-deoxyrhamnonate (L-KDR) into pyruvate and L-lactaldehyde, which is the last step of the Rha pathway. Deletion of lkaA resulted in impaired growth on L-rhamnose, and potentially in accumulation of L-KDR. Contrary to ΔlraA, ΔlrlA and ΔlrdA, the expression of the Rha-responsive genes that are under control of RhaR, were at the same levels in ΔlkaA and the reference strain, indicating the role of L-KDR as the inducer of the Rha pathway regulator.

CRISPR/Cas9 facilitates rapid generation of constitutive forms of transcription factors in Aspergillus niger through specific on-site genomic mutations resulting in increased saccharification of plant biomass

The CRISPR/Cas9 system has been successfully applied for gene editing in filamentous fungi. Previous studies reported that single stranded oligonucleotides can be used as repair templates to induce point mutations in some filamentous fungi belonging to genus Aspergillus. In Aspergillus niger, extensive research has been performed on regulation of plant biomass degradation, addressing transcription factors such as XlnR or GaaR, involved in (hemi-)cellulose and pectin utilization, respectively. Single nucleotide mutations leading to constitutively active forms of XlnR and GaaR have been previously reported. However, the mutations were performed by the introduction of versions obtained through site-directed or UV-mutagenesis into the genome. Here we report a more time- and cost-efficient approach to obtaining constitutively active versions by application of the CRISPR/Cas9 system to generate the desired mutation on-site in the A. niger genome. This was also achieved using only 60-mer single stranded oligonucleotides, shorter than the previously reported 90-mer strands. In this study, we show that CRISPR/Cas9 can also be used to efficiently change functional properties of the proteins encoded by the target gene by on-site genomic mutations in A. niger. The obtained strains with constitutively active XlnR and GaaR versions resulted in increased production of plant biomass degrading enzymes and improved release of d-xylose and l-arabinose from wheat bran, and d-galacturonic acid from sugar beet pulp.

Evolutionary adaptation of Aspergillus niger for increased ferulic acid tolerance

AIMS

To create an Aspergillus niger mutant with increased tolerance against ferulic acid using evolutionary adaptation.

METHODS AND RESULTS

Evolutionary adaptation of A. niger N402 was performed by consecutive growth on increasing concentrations of ferulic acid in the presence of 25 mmol l^-1 d-fructose, starting from 0·5 mmol l^-1 and ending with 5 mmol l^-1 ferulic acid. The A. niger mutant obtained after six months, named Fa6, showed increased ferulic acid tolerance compared to the parent. In addition, Fa6 has increased ferulic acid consumption and a higher conversion rate, suggesting that the mutation affects aromatic metabolism of this species. Transcriptome analysis of the evolutionary mutant on ferulic acid revealed a distinct gene expression profile compared to the wild type. Further analysis of this mutant and the parent strain provided the first experimental confirmation that A. niger converts coniferyl alcohol to ferulic acid.

CONCLUSIONS

The evolutionary adaptive A. niger mutant Fa6 has beneficial mutations that increase the tolerance, conversion rate and uptake of ferulic acid.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study demonstrates that evolutionary adaptation is a powerful tool to modify micro-organisms towards increased tolerance to harsh conditions, which is beneficial for various industrial applications.

Mild hydrothermal pretreatment of sugarcane bagasse enhances the production of holocellulases by Aspergillus niger

Holocellulase production by Aspergillus niger using raw sugarcane bagasse (rSCB) as the enzyme-inducing substrate is hampered by the intrinsic recalcitrance of this material. Here we report that mild hydrothermal pretreatment of rSCB increases holocellulase secretion by A. niger. Quantitative proteomic analysis revealed that pretreated solids (PS) induced a pronounced up-regulation of endoglucanases and cellobiohydrolases compared to rSCB, which resulted in a 10.1-fold increase in glucose release during SCB saccharification. The combined use of PS and pretreatment liquor (PL), referred to as whole pretreated slurry (WPS), as carbon source induced a more balanced up-regulation of cellulases, hemicellulases and pectinases and resulted in the highest increase (4.8-fold) in the release of total reducing sugars from SCB. The use of PL as the sole carbon source induced the modulation of A. niger's secretome towards hemicellulose degradation. Mild pretreatment allowed the use of PL in downstream biological operations without the need for undesirable detoxification steps.

Mapping the Secretome and Its N-Linked Glycosylation of Pleurotus eryngii and Pleurotus ostreatus Grown on Hemp Stalks

Our previous research showed that Pleurotus eryngii and Pleurotus ostreatus were effective fungi for pretreatment of industrial hemp stalks to improve enzymatic saccharification. The secretomes of these two fungi were analyzed to search for the effective enzyme cocktails degrading hemp lignin during the pretreatment process. In total, 169 and 155 proteins were identified in Pleurotus eryngii and Pleurotus ostreatus, respectively, and 50% of the proteins involved in lignocellulose degradation were CAZymes. Because most of the extracellular proteins secreted by fungi are glycosylated proteins, the N-linked glycosylation of enzymes could be mapped. In total, 27 and 24 N-glycosylated peptides were detected in Pleurotus eryngii and Pleurotus ostreatus secretomes, respectively. N-Glycosylated peptides of laccase, GH92, exoglucanase, phenol oxidase, α-galactosidase, carboxylic ester hydrolase, and pectin lyase were identified. Deglycosylation could decrease enzymatic saccharification of hemp stalks. The activities of laccase, α-galactosidase, and phenol oxidase and the thermal stability of laccase were reduced after deglycosylation.

Mutations in AraR leading to constitutive expression of arabinolytic genes in Aspergillus niger under derepressing conditions [corrected]

The AraR transcription factor of Aspergillus niger encodes a Zn(II)₂Cys₆ transcription factor required for the induction of genes encoding arabinolytic enzymes. One of the target genes of AraR is abfA, encoding an arabinofuranosidase. The expression of abfA as well as other L-arabinose-induced genes in A. niger requires the presence of L-arabinose or its derivative L-arabitol as an inducer to activate AraR-dependant gene expression. In this study, mutants were isolated that express L-arabinose-induced genes independently of the presence of an inducer under derepressing conditions. To obtain these mutants, a reporter strain was constructed in a ΔcreA background containing the L-arabinose-responsive promoter (PabfA) fused to the acetamidase (amdS) gene. Spores of the ΔcreA PabfA-amdS reporter strain were UV-mutagenized and mutants were obtained by their ability to grow on acetamide without the presence of inducer. From a total of 164 mutants, 15 mutants were identified to contain transacting mutations resulting in high arabinofuranosidase activity in the medium after growth under non-inducing conditions. Sequencing of the araR gene of the 15 constitutive mutants revealed that 14 mutants carried a mutation in AraR. Some mutations were found more than once and in total nine different point mutations were identified in AraR. The AraR^N806I point mutation was reintroduced into a parental strain and confirmed that this point mutation leads to inducer-independent expression of AraR target genes. The inducer independent of L-arabinose-induced genes in the AraR^N806I mutant was found to be sensitive to carbon catabolite repression, indicating that the CreA-mediated carbon catabolite repression is dominant over the AraR^N806I mutant allele. These mutations in AraR provide new opportunities to improve arabinase production in industrial fungal strains.

The presence of trace components significantly broadens the molecular response of Aspergillus niger to guar gum

Guar gum consists mainly of galactomannan and constitutes the endosperm of guar seeds that acts as a reserve polysaccharide for germination. Due to its molecular structure and physical properties, this biopolymer has been considered as one of the most important and widely used gums in industry. However, for many of these applications this (hemi-)cellulosic structure needs to be modified or (partially) depolymerized in order to customize and improve its physicochemical properties. In this study, transcriptome, exoproteome and enzyme activity analyses were employed to decipher the complete enzymatic arsenal for guar gum depolymerization by Aspergillus niger. This multi-omic analysis revealed a set of 46 genes encoding carbohydrate-active enzymes (CAZymes) responding to the presence of guar gum, including CAZymes not only with preferred activity towards galactomannan, but also towards (arabino-)xylan, cellulose, starch and pectin, likely due to trace components in guar gum. This demonstrates that the purity of substrates has a strong effect on the resulting enzyme mixture produced by A. niger and probably by other fungi as well, which has significant implications for the commercial production of fungal enzyme cocktails.

Spotlight on fungal pectin utilization-from phytopathogenicity to molecular recognition and industrial applications

Pectin is a complex polysaccharide with D-galacturonic acid as its main component that predominantly accumulates in the middle lamella of the plant cell wall. Integrity and depolymerization of pectic structures have long been identified as relevant factors in fungal phytosymbiosis and phytopathogenicity in the context of tissue penetration and carbon source supply. While the pectic content of a plant cell wall can vary significantly, pectin was reported to account for up to 20-25% of the total dry weight in soft and non-woody tissues with non- or mildly lignified secondary cell walls, such as found in citrus peel, sugar beet pulp, and apple pomace. Due to their potential applications in various industrial sectors, pectic sugars from these and similar agricultural waste streams have been recognized as valuable targets for a diverse set of biotechnological fermentations.Recent advances in uncovering the molecular regulation mechanisms for pectinase expression in saprophytic fungi have led to a better understanding of fungal pectin sensing and utilization that could help to improve industrial, pectin-based fermentations. Related research in phytopathogenic fungi has furthermore added to our knowledge regarding the relevance of pectinases in plant cell wall penetration during onset of disease and is therefore highly relevant for agricultural sciences and the agricultural industry. This review therefore aims at summarizing (i) the role of pectinases in phytopathogenicity, (ii) the global regulation patterns for pectinase expression in saprophytic filamentous fungi as a highly specialized class of pectin degraders, and (iii) the current industrial applications in pectic sugar fermentations and transformations.

A community-driven reconstruction of the Aspergillus niger metabolic network

Background

Aspergillus niger is an important fungus used in industrial applications for enzyme and acid production. To enable rational metabolic engineering of the species, available information can be collected and integrated in a genome-scale model to devise strategies for improving its performance as a host organism.

Results

In this paper, we update an existing model of A. niger metabolism to include the information collected from 876 publications, thereby expanding the coverage of the model by 940 reactions, 777 metabolites and 454 genes. In the presented consensus genome-scale model of A. niger iJB1325 , we integrated experimental data from publications and patents, as well as our own experiments, into a consistent network. This information has been included in a standardized way, allowing for automated testing and continuous improvements in the future. This repository of experimental data allowed the definition of 471 individual test cases, of which the model complies with 373 of them. We further re-analyzed existing transcriptomics and quantitative physiology data to gain new insights on metabolism. Additionally, the model contains 3482 checks on the model structure, thereby representing the best validated genome-scale model on A. niger developed until now. Strain-specific model versions for strains ATCC 1015 and CBS 513.88 have been created containing all data used for model building, thereby allowing users to adopt the models and check the updated version against the experimental data. The resulting model is compliant with the SBML standard and therefore enables users to easily simulate it using their preferred software solution.

Conclusion

Experimental data on most organisms are scattered across hundreds of publications and several repositories.To allow for a systems level understanding of metabolism, the data must be integrated in a consistent knowledge network. The A. niger iJB1325 model presented here integrates the available data into a highly curated genome-scale model to facilitate the simulation of flux distributions, as well as the interpretation of other genome-scale data by providing the metabolic context.

Electronic supplementary material

The online version of this article (10.1186/s40694-018-0060-7) contains supplementary material, which is available to authorized users.

In Silico Analysis of Putative Sugar Transporter Genes in Aspergillus niger Using Phylogeny and Comparative Transcriptomics

Aspergillus niger is one of the most widely used fungi to study the conversion of the lignocellulosic feedstocks into fermentable sugars. Understanding the sugar uptake system of A. niger is essential to improve the efficiency of the process of fungal plant biomass degradation. In this study, we report a comprehensive characterization of the sugar transportome of A. niger by combining phylogenetic and comparative transcriptomic analyses. We identified 86 putative sugar transporter (ST) genes based on a conserved protein domain search. All these candidates were then classified into nine subfamilies and their functional motifs and possible sugar-specificity were annotated according to phylogenetic analysis and literature mining. Furthermore, we comparatively analyzed the ST gene expression on a large set of fungal growth conditions including mono-, di- and polysaccharides, and mutants of transcriptional regulators. This revealed that transporter genes from the same phylogenetic clade displayed very diverse expression patterns and were regulated by different transcriptional factors. The genome-wide study of STs of A. niger provides new insights into the mechanisms underlying an extremely flexible metabolism and high nutritional versatility of A. niger and will facilitate further biochemical characterization and industrial applications of these candidate STs.

Induction of Genes Encoding Plant Cell Wall-Degrading Carbohydrate-Active Enzymes by Lignocellulose-Derived Monosaccharides and Cellobiose in the White-Rot Fungus Dichomitus squalens

Fungi can decompose plant biomass into small oligo- and monosaccharides to be used as carbon sources. Some of these small molecules may induce metabolic pathways and the production of extracellular enzymes targeted for degradation of plant cell wall polymers. Despite extensive studies in ascomycete fungi, little is known about the nature of inducers for the lignocellulolytic systems of basidiomycetes. In this study, we analyzed six sugars known to induce the expression of lignocellulolytic genes in ascomycetes for their role as inducers in the basidiomycete white-rot fungus Dichomitus squalens using a transcriptomic approach. This identified cellobiose and l-rhamnose as the main inducers of cellulolytic and pectinolytic genes, respectively, of D. squalens Our results also identified differences in gene expression patterns between dikaryotic and monokaryotic strains of D. squalens cultivated on plant biomass-derived monosaccharides and the disaccharide cellobiose. This suggests that despite conservation of the induction between these two genetic forms of D. squalens, the fine-tuning in the gene regulation of lignocellulose conversion is differently organized in these strains.IMPORTANCE Wood-decomposing basidiomycete fungi have a major role in the global carbon cycle and are promising candidates for lignocellulosic biorefinery applications. However, information on which components trigger enzyme production is currently lacking, which is crucial for the efficient use of these fungi in biotechnology. In this study, transcriptomes of the white-rot fungus Dichomitus squalens from plant biomass-derived monosaccharide and cellobiose cultures were studied to identify compounds that induce the expression of genes involved in plant biomass degradation.

The fungus Aspergillus niger consumes sugars in a sequential manner that is not mediated by the carbon catabolite repressor CreA

In nature, the fungus Aspergillus niger degrades plant biomass polysaccharides to monomeric sugars, transports them into its cells, and uses catabolic pathways to convert them into biochemical building blocks and energy. We show that when grown in liquid cultures, A. niger takes up plant-biomass derived sugars in a largely sequential manner. Interestingly, this sequential uptake was not mediated by the fungal general carbon catabolite repressor protein CreA. Furthermore, transcriptome analysis strongly indicated that the preferential use of the monomeric sugars is arranged at the level of transport, but it is not reflected in transcriptional regulation of sugar catabolism. Therefore, the results indicate that the regulation of sugar transport and catabolism are separate processes in A. niger.

Comparison of the paralogous transcription factors AraR and XlnR in Aspergillus oryzae

The paralogous transcription factors AraR and XlnR in Aspergillus regulate genes that are involved in degradation of cellulose and hemicellulose and catabolism of pentose. AraR and XlnR target the same genes for pentose catabolism but target different genes encoding enzymes for polysaccharide degradation. To uncover the relationship between these paralogous transcription factors, we examined their contribution to regulation of the PCP genes and compared their preferred recognition sequences. Both AraR and XlnR are involved in induction of all the pentose catabolic genes in A. oryzae except larA encoding L-arabinose reductase, which was regulated by AraR but not by XlnR. DNA-binding studies revealed that the recognition sequences of AraR and XlnR also differ only slightly; AraR prefers CGGDTAAW, while XlnR prefers CGGNTAAW. All the pentose catabolic genes possess at least one recognition site to which both AraR and XlnR can bind. Cooperative binding by the factors was not observed. Instead, they competed to bind to the shared sites. XlnR bound to the recognition sites mentioned above as a monomer, but bound to the sequence TTAGSCTAA on the xylanase promoters as a dimer. Consequently, AraR and XlnR have significantly similar, but not the same, DNA-binding properties. Such a slight difference in these paralogous transcription factors may lead to complex outputs in enzyme production depending on the concentrations of coexisting inducer molecules in the natural environment.