scholarly journals A Library of Aspergillus niger Chassis Strains for Morphology Engineering Connects Strain Fitness and Filamentous Growth With Submerged Macromorphology

2022 ◽  
Vol 9 ◽  
Author(s):  
Timothy C. Cairns ◽  
Xiaomei Zheng ◽  
Claudia Feurstein ◽  
Ping Zheng ◽  
Jibin Sun ◽  
...  
Keyword(s):  
Aspergillus Niger ◽  
Dry Weight ◽  
Filamentous Growth ◽  
Strain Engineering ◽  
Culture Conditions ◽  
Cell Factory ◽  
Fungal Cell ◽  
Cell Factories ◽  
Pellet Formation ◽  
Conditional Expression

Submerged fermentation using filamentous fungal cell factories is used to produce a diverse portfolio of useful molecules, including food, medicines, enzymes, and platform chemicals. Depending on strain background and abiotic culture conditions, different macromorphologies are formed during fermentation, ranging from dispersed hyphal fragments to approximately spherical pellets several millimetres in diameter. These macromorphologies are known to have a critical impact on product titres and rheological performance of the bioreactor. Pilot productivity screens in different macromorphological contexts is technically challenging, time consuming, and thus a significant limitation to achieving maximum product titres. To address this bottleneck, we developed a library of conditional expression mutants in the organic, protein, and secondary metabolite cell factory Aspergillus niger. Thirteen morphology-associated genes transcribed during fermentation were placed via CRISPR-Cas9 under control of a synthetic Tet-on gene switch. Quantitative analysis of submerged growth reveals that these strains have distinct and titratable macromorphologies for use as chassis during strain engineering programs. We also used this library as a tool to quantify how pellet formation is connected with strain fitness and filamentous growth. Using multiple linear regression modelling, we predict that pellet formation is dependent largely on strain fitness, whereas pellet Euclidian parameters depend on fitness and hyphal branching. Finally, we have shown that conditional expression of the putative kinase encoding gene pkh2 can decouple fitness, dry weight, pellet macromorphology, and culture heterogeneity. We hypothesize that further analysis of this gene product and the cell wall integrity pathway in which it is embedded will enable more precise engineering of A. niger macromorphology in future.

scholarly journals Vanillic acid and methoxyhydroquinone production from guaiacyl units and related aromatic compounds using Aspergillus niger cell factories

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Ronnie J. M. Lubbers ◽  
Adiphol Dilokpimol ◽  
Paula A. Nousiainen ◽  
Răzvan C. Cioc ◽  
Jaap Visser ◽  
...  
Keyword(s):  
Aspergillus Niger ◽  
Metabolic Pathway ◽  
Vanillic Acid ◽  
Aromatic Compounds ◽  
Metabolic Pathways ◽  
Fungal Cell ◽  
Cell Factories ◽  
Genes Encoding ◽  
Pharmaceutical Industries ◽  
Guaiacyl Lignin

Abstract Background The aromatic compounds vanillin and vanillic acid are important fragrances used in the food, beverage, cosmetic and pharmaceutical industries. Currently, most aromatic compounds used in products are chemically synthesized, while only a small percentage is extracted from natural sources. The metabolism of vanillin and vanillic acid has been studied for decades in microorganisms and many studies have been conducted that showed that both can be produced from ferulic acid using bacteria. In contrast, the degradation of vanillin and vanillic acid by fungi is poorly studied and no genes involved in this metabolic pathway have been identified. In this study, we aimed to clarify this metabolic pathway in Aspergillus niger and identify the genes involved. Results Using whole-genome transcriptome data, four genes involved in vanillin and vanillic acid metabolism were identified. These include vanillin dehydrogenase (vdhA), vanillic acid hydroxylase (vhyA), and two genes encoding novel enzymes, which function as methoxyhydroquinone 1,2-dioxygenase (mhdA) and 4-oxo-monomethyl adipate esterase (omeA). Deletion of these genes in A. niger confirmed their role in aromatic metabolism and the enzymatic activities of these enzymes were verified. In addition, we demonstrated that mhdA and vhyA deletion mutants can be used as fungal cell factories for the accumulation of vanillic acid and methoxyhydroquinone from guaiacyl lignin units and related aromatic compounds. Conclusions This study provides new insights into the fungal aromatic metabolic pathways involved in the degradation of guaiacyl units and related aromatic compounds. The identification of the involved genes unlocks new potential for engineering aromatic compound-producing fungal cell factories.

scholarly journals Updating genome annotation for the microbial cell factory Aspergillus niger using gene co-expression networks

2018 ◽  
Author(s):  
p Schäp ◽  
MJ Kwon ◽  
B Baumann ◽  
B Gutschmann ◽  
S Jung ◽  
...  
Keyword(s):  
Aspergillus Niger ◽  
Fungal Pathogens ◽  
Meta Analysis ◽  
Microbial Cell ◽  
Model Systems ◽  
Model Organisms ◽  
Cell Factory ◽  
Microbial Cell Factory ◽  
Cell Factories ◽  
Promising Source

AbstractA significant challenge in our understanding of biological systems is the high number of genes with unknown function in many genomes. The fungal genus Aspergillus contains important pathogens of humans, model organisms, and microbial cell factories. Aspergillus niger is used to produce organic acids, proteins, and is a promising source of new bioactive secondary metabolites. Out of the 14,165 open reading frames predicted in the A. niger genome of only 2% have been experimentally verified and over 6,000 are hypothetical. Here we show that gene co-expression network analysis can be used to overcome this limitation. A meta-analysis of 155 transcriptomics experiments generated co-expression networks for 9,579 genes (∼65%) of the A. niger genome. By populating this dataset with over 1,200 gene functional experiments from the genus Aspergillus and performing gene ontology enrichment, we could infer biological processes for 9,263 of A. niger genes, including 2,970 hypothetical genes. Experimental validation of selected co-expression sub-networks uncovered four transcription factors involved in secondary metabolite synthesis, which were used to activate production of multiple natural products. This study constitutes a significant step towards systems-level understanding of A. niger, and the datasets can be used to fuel discoveries of model systems, fungal pathogens, and biotechnology.

scholarly journals Enzymatic Hydrolysate of Cinnamon Waste Material as Feedstock for the Microbial Production of Carotenoids

2021 ◽  
Vol 18 (3) ◽  
pp. 1146
Author(s):  
Stefano Bertacchi ◽  
Stefania Pagliari ◽  
Chiara Cantù ◽  
Ilaria Bruni ◽  
Massimo Labra ◽  
...  
Keyword(s):  
Industrial Sector ◽  
Waste Material ◽  
Fungal Cell ◽  
Enzymatic Hydrolysate ◽  
Carbon And Nitrogen ◽  
Microbial Cell Factories ◽  
Cell Factories ◽  
Separate Hydrolysis And Fermentation ◽  
Additional Processing ◽  
Microbial Cultivation

In the context of the global need to move towards circular economies, microbial cell factories can be employed thanks to their ability to use side-stream biomasses from the agro-industrial sector to obtain additional products. The valorization of residues allows for better and complete use of natural resources and, at the same time, for the avoidance of waste management to address our needs. In this work, we focused our attention on the microbial valorization of cinnamon waste material after polyphenol extraction (C-PEW) (Cinnamomum verum J.Presl), generally discarded without any additional processing. The sugars embedded in C-PEW were released by enzymatic hydrolysis, more compatible than acid hydrolysis with the subsequent microbial cultivation. We demonstrated that the yeast Rhodosporidium toruloides was able to grow and produce up to 2.00 (±0.23) mg/L of carotenoids in the resulting hydrolysate as a sole carbon and nitrogen source despite the presence of antimicrobial compounds typical of cinnamon. To further extend the potential of our finding, we tested other fungal cell factories for growth on the same media. Overall, these results are opening the possibility to develop separate hydrolysis and fermentation (SHF) bioprocesses based on C-PEW and microbial biotransformation to obtain high-value molecules.

Lysis and biological control of Aspergillus niger by Bacillus subtilis AF 1

1996 ◽  
Vol 42 (6) ◽  
pp. 533-538 ◽  
Author(s):  
A. R. Podile ◽  
A. P. Prakash
Keyword(s):  
Biological Control ◽  
Bacillus Subtilis ◽  
Aspergillus Niger ◽  
Fungal Growth ◽  
Dry Weight ◽  
Crown Rot ◽  
Fungal Mycelium ◽  
Infested Soil ◽  
Dual Culture ◽  
Bacterial Cells

A biocontrol rhizobacterial strain of Bacillus subtilis AF 1 grown for 6 h was coinoculated with Aspergillus niger at different time intervals and microscopic observations revealed adherence of bacterial cells to the fungal mycelium. Bacterial cells multiplied in situ and colonized the mycelial surface. Growth of AF 1 resulted in damage to the cell wall, followed by lysis. AF 1 inoculation into media containing A. niger at 0, 6, and 12 h suppressed >90% fungal growth, while in 18- and 24-h cultures fungal growth inhibition was 70 and 56%, respectively, in terms of dry weight. In dual culture the fungal growth was not accompanied by formation of spores. The mycelial preparation of A. niger as principal carbon source supported the growth of B. subtilis, as much as chitin. Extracellular protein precipitate from B. subtilis culture filtrate had a significant growth-retarding effect on A. niger. Groundnut seeds bacterized with B. subtilis showed a reduced incidence of crown rot in A. niger infested soil, suggesting a possible role of B. subtilis in biological control of A. niger.Key words: mycolytic bacteria, Bacillus subtilis, Aspergillus niger, biological control.

scholarly journals Nanocellulose-based mechanically stable immobilization matrix for enhanced ethylene production: A framework for photosynthetic solid-state cell factories

2021 ◽  
Author(s):  
Ville Rissanen ◽  
Sindhujaa Vajravel ◽  
Sergey Kosourov ◽  
Suvi Arola ◽  
Eero Kontturi ◽  
...  
Keyword(s):  
Solid State ◽  
Ethylene Production ◽  
Cell Immobilization ◽  
Cell Factory ◽  
Cell Factories ◽  
Solid State Cell ◽  
Immobilization Matrix

Cell immobilization is a promising approach to create efficient photosynthetic cell factories for sustainable chemicals production. Here, we demonstrate a novel photosynthetic solid-state cell factory design for sustainable biocatalytic ethylene...

Characterization of a novel Aspergillus niger beta-glucosidase tolerant to saccharification of lignocellulosic biomass products and fermentation inhibitors

2015 ◽  
Vol 69 (8) ◽  
Author(s):  
Alesandra Oriente ◽  
Robson Tramontina ◽  
Diandra de Andrades ◽  
Caroline Henn ◽  
Jose L. C. Silva ◽  
...  
Keyword(s):  
Aspergillus Niger ◽  
Lignocellulosic Biomass ◽  
Culture Conditions ◽  
Industrial Wastes ◽  
Fermentation Inhibitors ◽  
State Culture ◽  
Solid State Culture ◽  
Atlantic Rainforest Biome ◽  
Beta Glucosidase

AbstractProperties of beta-glucosidase produced by Aspergillus niger URM 6642 recently isolated from the Atlantic rainforest biome and its potential tolerance to saccharification of lignocellulosic biomass products and fermentation inhibitors was evaluated. The fungus was cultivated under solid state culture conditions at 37°C with different agro-industrial wastes. High levels of beta-glucosidase (3778.9 U g

scholarly journals Mitochondrial perturbation reduces susceptibility to xenobiotics through altered efflux in Candida albicans

Genetics ◽  
2021 ◽  
Author(s):  
Saif Hossain ◽  
Amanda O Veri ◽  
Zhongle Liu ◽  
Kali R Iyer ◽  
Teresa R O’Meara ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Mitochondrial Function ◽  
Efflux Pump ◽  
Systemic Disease ◽  
Filamentous Growth ◽  
Hsp90 Inhibitor ◽  
Homozygous Deletion ◽  
Hsp90 Inhibitors ◽  
Hsp90 Inhibition ◽  
Conditional Expression

Abstract Candida albicans is a leading human fungal pathogen, which can cause superficial infections or life-threatening systemic disease in immunocompromised individuals. The ability to transition between yeast and filamentous forms is a major virulence trait of C. albicans, and a key regulator of this morphogenetic transition is the molecular chaperone Hsp90. To explore the mechanisms governing C. albicans morphogenesis in response to Hsp90 inhibition, we performed a functional genomic screen using the gene replacement and conditional expression (GRACE) collection to identify mutants that are defective in filamentation in response to the Hsp90 inhibitor, geldanamycin. We found that transcriptional repression of genes involved in mitochondrial function blocked filamentous growth in response to the concentration of Hsp90 inhibitor used in the screen, and this was attributable to increased resistance to the compound. Further exploration revealed that perturbation of mitochondrial function reduced susceptibility to two structurally distinct Hsp90 inhibitors, geldanamycin and radicicol, such that filamentous growth was restored in the mitochondrial mutants by increasing the compound concentration. Deletion of two representative mitochondrial genes, MSU1 and SHY1, enhanced cellular efflux and reduced susceptibility to diverse intracellularly acting compounds. Additionally, screening a C. albicans efflux pump gene deletion library implicated Yor1 in efflux of geldanamycin and Cdr1, in efflux of radicicol. Deletion of these transporter genes restored sensitivity to Hsp90 inhibitors in MSU1 and SHY1 homozygous deletion mutants, thereby enabling filamentation. Taken together, our findings suggest that mitochondrial dysregulation elevates cellular efflux and consequently reduces susceptibility to xenobiotics in C. albicans.

scholarly journals A squalene–hopene cyclase in Schizosaccharomyces japonicus represents a eukaryotic adaptation to sterol-limited anaerobic environments

2021 ◽  
Vol 118 (32) ◽  
pp. e2105225118
Author(s):  
Jonna Bouwknegt ◽  
Sanne J. Wiersma ◽  
Raúl A. Ortiz-Merino ◽  
Eline S. R. Doornenbal ◽  
Petrik Buitenhuis ◽  
...  
Keyword(s):  
Unsaturated Fatty Acids ◽  
Yeast Species ◽  
Early Report ◽  
Anaerobic Growth ◽  
Fungal Cell ◽  
Putative Gene ◽  
Cell Factories ◽  
Lipid Fractions ◽  
Synthetic Media ◽  
Free Media

Biosynthesis of sterols, which are key constituents of canonical eukaryotic membranes, requires molecular oxygen. Anaerobic protists and deep-branching anaerobic fungi are the only eukaryotes in which a mechanism for sterol-independent growth has been elucidated. In these organisms, tetrahymanol, formed through oxygen-independent cyclization of squalene by a squalene–tetrahymanol cyclase, acts as a sterol surrogate. This study confirms an early report [C. J. E. A. Bulder, Antonie Van Leeuwenhoek, 37, 353–358 (1971)] that Schizosaccharomyces japonicus is exceptional among yeasts in growing anaerobically on synthetic media lacking sterols and unsaturated fatty acids. Mass spectrometry of lipid fractions of anaerobically grown Sch. japonicus showed the presence of hopanoids, a class of cyclic triterpenoids not previously detected in yeasts, including hop-22(29)-ene, hop-17(21)-ene, hop-21(22)-ene, and hopan-22-ol. A putative gene in Sch. japonicus showed high similarity to bacterial squalene–hopene cyclase (SHC) genes and in particular to those of Acetobacter species. No orthologs of the putative Sch. japonicus SHC were found in other yeast species. Expression of the Sch. japonicus SHC gene (Sjshc1) in Saccharomyces cerevisiae enabled hopanoid synthesis and stimulated anaerobic growth in sterol-free media, thus indicating that one or more of the hopanoids produced by SjShc1 could at least partially replace sterols. Use of hopanoids as sterol surrogates represents a previously unknown adaptation of eukaryotic cells to anaerobic growth. The fast anaerobic growth of Sch. japonicus in sterol-free media is an interesting trait for developing robust fungal cell factories for application in anaerobic industrial processes.

scholarly journals Computational Analysis of Dynamic Light Exposure of Unicellular Algal Cells in a Flat-Panel Photobioreactor to Support Light-Induced CO2 Bioprocess Development

2021 ◽  
Vol 12 ◽  
Author(s):  
Nicolò S. Vasile ◽  
Alessandro Cordara ◽  
Giulia Usai ◽  
Angela Re
Keyword(s):  
Light Transmission ◽  
Light Exposure ◽  
Model Organism ◽  
Cell Factory ◽  
Bioprocess Development ◽  
Cultivation Conditions ◽  
Flat Panel ◽  
Modeling Framework ◽  
Cell Factories ◽  
Cell Trajectories

Cyanobacterial cell factories trace a vibrant pathway to climate change neutrality and sustainable development owing to their ability to turn carbon dioxide-rich waste into a broad portfolio of renewable compounds, which are deemed valuable in green chemistry cross-sectorial applications. Cell factory design requires to define the optimal operational and cultivation conditions. The paramount parameter in biomass cultivation in photobioreactors is the light intensity since it impacts cellular physiology and productivity. Our modeling framework provides a basis for the predictive control of light-limited, light-saturated, and light-inhibited growth of the Synechocystis sp. PCC 6803 model organism in a flat-panel photobioreactor. The model here presented couples computational fluid dynamics, light transmission, kinetic modeling, and the reconstruction of single cell trajectories in differently irradiated areas of the photobioreactor to relate key physiological parameters to the multi-faceted processes occurring in the cultivation environment. Furthermore, our analysis highlights the need for properly constraining the model with decisive qualitative and quantitative data related to light calibration and light measurements both at the inlet and outlet of the photobioreactor in order to boost the accuracy and extrapolation capabilities of the model.

scholarly journals Infection with intracellular parasite Amoeboaphelidium protococcarum induces shifts in associated bacterial communities in microalgae cultures

2021 ◽  
Vol 33 (5) ◽  
pp. 2863-2873
Author(s):  
Anna-Lena Höger ◽  
Carola Griehl ◽  
Matthias Noll
Keyword(s):  
Bacterial Communities ◽  
Large Scale ◽  
Algal Growth ◽  
Dry Weight ◽  
Illumina Miseq ◽  
Culture Conditions ◽  
Rrna Gene ◽  
Scale Production ◽  
Market Demand ◽  
Freshwater Microalgae

AbstractIn recent years microalgae products have developed increasing market demand, but sustainable industrial production is still challenged by biological stability of large-scale production plants. Yet the relationships between algal hosts, associated microbiomes, and contaminants in photobioreactors remains widely understudied. The aim of this study was to investigate the temporal development of microbiomes of four freshwater microalgae species Scenedesmus vacuolatus, Desmodesmus quadricauda, Chlorella sorokiniana, and Botryococcus braunii, in presence and absence of the zoosporic parasite Amoeboaphelidium protococcarum. To compare the effects of sterile and nonsterile culture conditions, infection experiments were performed in sterile laboratory (sterile) and simulated industrial conditions (open). Algal growth (dry weight, optical density, and nutrient consumption) was observed for 21 days, and samples of the associated microbiome were collected for bacterial 16S rRNA gene Illumina MiSeq sequencing. Infection patterns of A. protococcarum were algae species-specific, irrespectively of culture conditions. Bacterial community analysis demonstrated distinct and stable bacterial communities for each algae species, which were mostly dominated by α- and γ-Proteobacteria. Upon aphelid parasitosis, bacterial diversity increased, and community compositions diverged algae-specific over time. Moreover, bacterial functional traits shifted to detoxification, degradation, and cellulolysis once algae were infected. This study provides a first insight into the close connection between algae, associated bacterial microbiomes and appearing contaminants in photobioreactor systems.

Sign in / Sign up

Export Citation Format

Share Document