9 Transcriptomics of Industrial Filamentous Fungi: A New View on Regulation, Physiology, and Application

Nitsche, Benjamin; Meyer, Vera

doi:10.1007/978-3-642-45218-5_9

Cited by 3 publications

(2 citation statements)

References 131 publications

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“…An outstanding opportunity to study the biological function(s) of antifungal peptides for their producing fungus is to scrutinize the growing body of system biology data. The antifungal peptide AnAFP from A. niger represents an excellent model system for several reasons: Firstly, the genome of A. niger has been sequenced [ 38 ], and hundreds of transcriptomics and proteomics data are publicly available for the A. niger strain CBS 513.88 and its derivatives [ 39 , 40 ] (note that the genome of A. giganteus has not been sequenced yet). Secondly, various bioinformatics pipelines for the analysis of genomic and transcriptomic data are available for A. niger [ 41 , 42 ].…”

Section: Gene Regulation Of Afp-encoding Genes: From the General Tmentioning

confidence: 99%

Antifungal Peptides of the AFP Family Revisited: Are These Cannibal Toxins?

Meyer

Jung

2018

Microorganisms

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The emergence and spread of pathogenic fungi resistant to currently used antifungal drugs represents a serious challenge for medicine and agriculture. The use of smart antimicrobials, so-called “dirty drugs” which affect multiple cellular targets, is one strategy to prevent resistance. Of special interest is the exploitation of the AFP family of antimicrobial peptides, which include its founding member AFP from Aspergillus giganteus. This latter is a highly potent inhibitor of chitin synthesis and affects plasma membrane integrity in many human and plant pathogenic fungi. A transcriptomic meta-analysis of the afp-encoding genes in A. giganteus and A. niger predicts a role for these proteins during asexual sporulation, autophagy, and nutrient recycling, suggesting that AFPs are molecules important for the survival of A. niger and A. giganteus under nutrient limitation. In this review, we discuss parallels which exist between AFPs and bacterial cannibal toxins and provide arguments that the primary function of AFPs could be to kill genetically identical siblings. We hope that this review inspires computational and experimental biologists studying alternative explanations for the nature and function of antimicrobial peptides beyond the general assumption that they are mere defense molecules to fight competitors.

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Section: Gene Regulation Of Afp-encoding Genes: From the General Tmentioning

confidence: 99%

Antifungal Peptides of the AFP Family Revisited: Are These Cannibal Toxins?

Meyer

Jung

2018

Microorganisms

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“…niger strain CBS 513.88 belongs to the best annotated Aspergillus genomes [16] and hundreds of transcriptomics and proteomics data have been published for this strain. Genome-wide expression profiles of strain CBS 513.88 were published for different cultivation conditions, developmental stages and environmental stress conditions (for reviews see [17, 18], thus constituting an invaluable treasure chest which can be systematically mined for expression of the anafp gene. Finally, we have developed various bioinformatics pipelines for the analysis of genomic and transcriptomic data of A .…”

Section: Introductionmentioning

confidence: 99%

A Transcriptome Meta-Analysis Proposes Novel Biological Roles for the Antifungal Protein AnAFP in Aspergillus niger

Paege¹,

Jung²,

Schäpe³

et al. 2016

PLoS ONE

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Understanding the genetic, molecular and evolutionary basis of cysteine-stabilized antifungal proteins (AFPs) from fungi is important for understanding whether their function is mainly defensive or associated with fungal growth and development. In the current study, a transcriptome meta-analysis of the Aspergillus niger γ-core protein AnAFP was performed to explore co-expressed genes and pathways, based on independent expression profiling microarrays covering 155 distinct cultivation conditions. This analysis uncovered that anafp displays a highly coordinated temporal and spatial transcriptional profile which is concomitant with key nutritional and developmental processes. Its expression profile coincides with early starvation response and parallels with genes involved in nutrient mobilization and autophagy. Using fluorescence- and luciferase reporter strains we demonstrated that the anafp promoter is active in highly vacuolated compartments and foraging hyphal cells during carbon starvation with CreA and FlbA, but not BrlA, as most likely regulators of anafp. A co-expression network analysis supported by luciferase-based reporter assays uncovered that anafp expression is embedded in several cellular processes including allorecognition, osmotic and oxidative stress survival, development, secondary metabolism and autophagy, and predicted StuA and VelC as additional regulators. The transcriptomic resources available for A. niger provide unparalleled resources to investigate the function of proteins. Our work illustrates how transcriptomic meta-analyses can lead to hypotheses regarding protein function and predict a role for AnAFP during slow growth, allorecognition, asexual development and nutrient recycling of A. niger and propose that it interacts with the autophagic machinery to enable these processes.

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The Cell Factory Aspergillus Enters the Big Data Era: Opportunities and Challenges for Optimising Product Formation

Meyer¹,

Fiedler²,

Nitsche³

et al. 2015

Advances in Biochemical Engineering/Biotechnology

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Living with limits. Getting more from less. Producing commodities and high-value products from renewable resources including waste. What is the driving force and quintessence of bioeconomy outlines the lifestyle and product portfolio of Aspergillus, a saprophytic genus, to which some of the top-performing microbial cell factories belong: Aspergillus niger, Aspergillus oryzae and Aspergillus terreus. What makes them so interesting for exploitation in biotechnology and how can they help us to address key challenges of the twenty-first century? How can these strains become trimmed for better growth on second-generation feedstocks and how can we enlarge their product portfolio by genetic and metabolic engineering to get more from less? On the other hand, what makes it so challenging to deduce biological meaning from the wealth of Aspergillus -omics data? And which hurdles hinder us to model and engineer industrial strains for higher productivity and better rheological performance under industrial cultivation conditions? In this review, we will address these issues by highlighting most recent findings from the Aspergillus research with a focus on fungal growth, physiology, morphology and product formation. Indeed, the last years brought us many surprising insights into model and industrial strains. They clearly told us that similar is not the same: there are different ways to make a hypha, there are more protein secretion routes than anticipated and there are different molecular and physical mechanisms which control polar growth and the development of hyphal networks. We will discuss new conceptual frameworks derived from these insights and the future scientific advances necessary to create value from Aspergillus Big Data.

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9 Transcriptomics of Industrial Filamentous Fungi: A New View on Regulation, Physiology, and Application

Cited by 3 publications

References 131 publications

Antifungal Peptides of the AFP Family Revisited: Are These Cannibal Toxins?

Antifungal Peptides of the AFP Family Revisited: Are These Cannibal Toxins?

A Transcriptome Meta-Analysis Proposes Novel Biological Roles for the Antifungal Protein AnAFP in Aspergillus niger

The Cell Factory Aspergillus Enters the Big Data Era: Opportunities and Challenges for Optimising Product Formation

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