Article
Biotechnology & Applied Microbiology
Ronnie J. M. Lubbers, Adiphol Dilokpimol, Jaap Visser, Kristiina S. Hilden, Miia R. Makela, Ronald P. de Vries
Summary: Salicylic acid plays a crucial role in the plant immune response and its degradation is important for plant-pathogenic fungi. In the filamentous fungus Aspergillus niger, two metabolic pathways for salicylic acid have been suggested. This study identified genes involved in salicylic acid metabolism in A. niger and confirmed the function of ShyA and CrcA in converting salicylic acid to cis,cis-muconic acid. The findings offer insights into efficient utilization of plant biomass and alternative methods for producing platform chemicals like cis,cis-muconic acid.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Genetics & Heredity
Sandra Garrigues, Roland S. Kun, Ronald P. de Vries
Summary: This study examines the use of genetic barcodes to trace genetically modified organisms (GMOs) and found that both barcoded and non-barcoded mutants can be traced effectively through routine PCR reactions. The presence of barcodes did not affect the efficiency of genetic modification or the growth and protein production of resulting strains, confirming their suitability for tracing CRISPR-derived GMOs without impacting performance.
Article
Biotechnology & Applied Microbiology
Ronnie J. M. Lubbers, Adiphol Dilokpimol, Paula A. Nousiainen, Jaap Visser, Pieter C. A. Bruijnincx, Ronald P. de Vries, Razvan C. Cioc
Summary: This study identified four genes involved in vanillin and vanillic acid metabolism in Aspergillus niger using whole-genome transcriptome data. Deletion of these genes confirmed their role in aromatic metabolism and the enzymatic activities of these enzymes were verified. Deletion mutants of mhdA and vhyA can be used as fungal cell factories for the accumulation of vanillic acid and methoxyhydroquinone from guaiacyl lignin units and related aromatic compounds, providing new insights into fungal aromatic metabolic pathways.
MICROBIAL CELL FACTORIES
(2021)
Article
Microbiology
Ronnie J. M. Lubbers, Ronald P. de Vries
Summary: Protocatechuic acid is an important chemical building block with pharmaceutical properties that can also be used to produce polymers and plastics. By identifying protocatechuate hydroxylase, it was found that a fungal cell factory can accumulate protocatechuic acid from plant-derived aromatic compounds. This research contributes to creating alternative methods for producing valuable aromatic compounds and platform chemicals.
Article
Biochemical Research Methods
Xinxin Li, Dimitrios Kouzounis, Mirjam A. Kabel, Ronald P. de Vries, Adiphol Dilokpimol
Summary: Efficient bioconversion of agro-industrial side streams requires a wide range of enzyme activities. This study focused on the GH30 family of enzymes and identified novel enzyme activities within this diverse family. A phylogenetic tree was constructed, showing that GH30 enzymes cluster into four subfamilies with distinct polysaccharide specificities and high potential for the production of short non-digestible di- and oligosaccharides.
Article
Biochemistry & Molecular Biology
Mila Marinovic, Marcos Di Falco, Maria Victoria Aguilar Pontes, Andras Gorzsas, Adrian Tsang, Ronald P. de Vries, Miia R. Makela, Kristiina Hilden
Summary: The unique ability of basidiomycete white rot fungi to degrade all components of plant cell walls makes them essential in the global carbon cycle. This study analyzed the proteomes of two closely related white rot fungi during cultivation on solid spruce wood, revealing specific enzymes produced during the degradation process. These findings provide valuable insights into enzyme production in nature and their potential use in biotechnological applications.
Article
Soil Science
Svenja C. Stock, Moritz Koester, Francisco Najera, Jens Boy, Francisco Matus, Carolina Merino, Khaled Abdallah, Sandra Spielvogel, Anna A. Gorbushina, Michaela A. Dippold, Yakov Kuzyakov
Summary: The nutrient acquisition strategies of plants, particularly regarding nitrogen and potassium, vary depending on the environmental conditions and habitats. The accessibility of nutrients in the topsoil influences the plants' ability to absorb nutrients from deeper soil layers, thereby regulating water flow and mass transport within ecosystems.
Article
Biochemistry & Molecular Biology
Jiali Meng, Miia R. Maekelae, Ronald P. de Vries
Summary: In this study, an l-arabitol transporter, LatA, was identified in Aspergillus niger. It was found that LatA only imports l-arabitol and is regulated by the arabinanolytic transcriptional activator AraR. Deletion of latA can increase l-arabitol production, indicating its potential for improving l-arabitol-producing cell factories. Phylogenetic analysis showed that homologs of LatA are widely conserved in fungi.
Article
Microbiology
Roland S. Kun, Sonia Salazar-Cerezo, Mao Peng, Yu Zhang, Emily Savage, Anna Lipzen, Vivian Ng, Igor V. Grigoriev, Ronald P. de Vries, Sandra Garrigues
Summary: This study deepened the understanding of the storage polysaccharide regulators AmyR and InuR in Aspergillus niger by assessing the phenotypes and transcriptomic data of different strains under various culture conditions. The results showed that AmyR has a minor contribution to sucrose and inulin utilization when InuR is active, and deletion of amyR in the Delta inuR background strain resulted in pronounced growth reduction on both substrates, particularly in solid cultures. Overall, the study highlights the importance of culture conditions in accurately studying the role of transcription factors in filamentous fungi.
Review
Biotechnology & Applied Microbiology
Dujuan Liu, Sandra Garrigues, Ronald P. de Vries
Summary: The article summarizes the benefits and challenges of using filamentous fungi for the production of heterologous proteins, as well as various techniques commonly employed to improve the production yield. These techniques include the use of strong and inducible promoters, codon optimization, more efficient signal peptides for secretion, carrier proteins, engineering of glycosylation sites, regulation of the unfolded protein response and endoplasmic reticulum associated protein degradation, optimization of the intracellular transport process, regulation of unconventional protein secretion, and construction of protease-deficient strains.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Microbiology
Sandra Garrigues, Mao Peng, Roland S. S. Kun, Ronald P. de Vries
Summary: CRISPR/Cas9 genome editing technology has been widely used in various organisms, but off-target mutations may occur due to guide RNA binding to similar nucleotides. Despite this, evaluation of mutations is rarely performed in genome editing studies.
Review
Microbiology
Sonia Salazar-Cerezo, Ronald P. de Vries, Sandra Garrigues
Summary: The use of microorganisms in industry allows for the mass production of various compounds relevant to antibiotics, food, beverages, cosmetics, chemicals, and biofuels. Traditional strain improvement and random screening are commonly used to obtain industrial strains, but recombinant DNA technology has enabled the improvement of microbial strains by gene manipulation. Genetic engineering, genome editing, and other techniques are contributing to the development of fungal production strains. This review discusses classical and recent methods, tools, and technologies used to develop fungal production strains for industrial applications, as well as the use of functional genomics and other omics technologies in combination with genetic manipulation techniques.
Article
Microbiology
Jiajia Li, Ad Wiebenga, Anna Lipzen, Vivian Ng, Sravanthi Tejomurthula, Yu Zhang, Igor V. Grigoriev, Mao Peng, Ronald P. de Vries
Summary: This study systematically compared the genomic content and transcriptional dynamics of carbohydrate-active enzymes (CAZymes) in six taxonomically distant fungal species during growth on nine monosaccharides. It identified considerable genomic variation and remarkable transcriptomic diversity of CAZymes, implying the preferred carbon source of these fungi and their different methods of transcription regulation.
Article
Materials Science, Multidisciplinary
Romy Breitenbach, Ruben Gerrits, Polina Dementyeva, Nicole Knabe, Julia Schumacher, Ines Feldmann, Jorg Radnik, Masahiro Ryo, Anna A. Gorbushina
Summary: The roles of extracellular polymeric substances (EPS) in mineral attachment and weathering were investigated using genetically modified biofilms of Knufia petricola strain A95. Mutants deficient in melanin and/or carotenoid synthesis were grown as air-exposed biofilms. The presence of melanin affected the quantity and composition of EPS, with melanin-producing strains showing stronger attachment to the mineral olivine and faster dissolution rates. The pullulan-related glycosidic linkages in EPS enable fungal attachment and weathering, while phenolic intermediates released by melanin synthesis may enhance olivine dissolution. These findings highlight the importance of compositional and quantitative analyses of biofilm microenvironments.
NPJ MATERIALS DEGRADATION
(2022)
Article
Mycology
Eileen A. Erdmann, Sarah Nitsche, Anna A. Gorbushina, Julia Schumacher
Summary: Black microcolonial fungi, stress-tolerant and persistent dwellers in extreme habitats, can now be studied using advanced genetic tools for a more detailed understanding of their survival mechanisms and interactions.
FRONTIERS IN FUNGAL BIOLOGY
(2022)
