ArticleGenome biology2009
Systemic analysis of the response of Aspergillus niger to ambient pH.
Article in Genome biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
48 citing papers in PubMed.
- EngineeredSynthetic and systems biotechnology · 2026Article
- Harnessing the power of abiotic inducers to enhance fungal secondary metabolite production: a review.Folia microbiologica · 2026Review
- Iodine Accumulation and Biovolatilization by Filamentous Fungi and Their Effects on Extracellular Organic Acids.Journal of fungi (Basel, Switzerland) · 2026Article
- Climate change-driven geographical shifts iniScience · 2026Article
- Understanding the Role of pH Regulation and Neutralizing Agents in Organic Acid Production and Growth of Aspergillus oryzae.Biotechnology and bioengineering · 2026Article
- Transcriptional Responses to Alkaline pH Across Fungi: Common and Differential Features, and Biotechnological Applications.International journal of molecular sciences · 2025Review
- Metabolite profiling and adaptation mechanisms ofFrontiers in microbiology · 2025Article
- Methods for studying microbial acid stress responses: from molecules to populations.FEMS microbiology reviews · 2024Review
- Article
- Citric Acid: Properties, Microbial Production, and Applications in Industries.Molecules (Basel, Switzerland) · 2023Review
- Article
- Physiological mechanisms by which gypsum increases the growth and yield of Lentinula edodes.Applied microbiology and biotechnology · 2022Article
- Organic acid, a virulence factor for pathogenic fungi, causing postharvest decay in fruits.Molecular plant pathology · 2022Review
- Soil bacteria protect fungi from phenazines by acting as toxin sponges.Current biology : CB · 2022Article
- Fungal Mobilization of Selenium in the Presence of Hausmannite and Ferric Oxyhydroxides.Journal of fungi (Basel, Switzerland) · 2021Article
- Turning Inside Out: Filamentous Fungal Secretion and Its Applications in Biotechnology, Agriculture, and the Clinic.Journal of fungi (Basel, Switzerland) · 2021Review
- Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions.Microbial cell factories · 2021Article
- Global Transcriptional Response ofJournal of fungi (Basel, Switzerland) · 2021Article
- Metabolic engineering of Aspergillus niger via ribonucleoprotein-based CRISPR-Cas9 system for succinic acid production from renewable biomass.Biotechnology for biofuels · 2020Article
- Challenging the charge balance hypothesis: reconsidering buffer effect and reuptake of previously excreted organic acids by Penicillium ochrochloron.FEMS microbiology letters · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe filamentous fungus Aspergillus niger is an exceptionally efficient producer of organic acids, which is one of the reasons for its relevance to industrial processes and commercial importance. While it is known that the mechanisms regulating this production are tied to the levels of ambient pH, the reasons and mechanisms for this are poorly understood.
methodsTo cast light on the connection between extracellular pH and acid production, we integrate results from two genome-based strategies: A novel method of genome-scale modeling of the response, and transcriptome analysis across three levels of pH.
resultsWith genome scale modeling with an optimization for extracellular proton-production, it was possible to reproduce the preferred pH levels for citrate and oxalate. Transcriptome analysis and clustering expanded upon these results and allowed the identification of 162 clusters with distinct transcription patterns across the different pH-levels examined. New and previously described pH-dependent cis-acting promoter elements were identified. Combining transcriptome data with genomic coordinates identified four pH-regulated secondary metabolite gene clusters. Integration of regulatory profiles with functional genomics led to the identification of candidate genes for all steps of the pal/pacC pH signalling pathway.
conclusionsThe combination of genome-scale modeling with comparative genomics and transcriptome analysis has provided systems-wide insights into the evolution of highly efficient acidification as well as production process applicable knowledge on the transcriptional regulation of pH response in the industrially important A. niger. It has also made clear that filamentous fungi have evolved to employ several offensive strategies for out-competing rival organisms.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.