Transcriptomics

Dataset Information

11

Submerged differentiation of Aspergillus niger in carbon-limited cultures approaching zero specific growth rate


ABSTRACT: This work presents an exploration of submerged differentiation of the ubiquitous saprophyte and industrially important fungus, Aspergillus niger, in response to a limited availability of a sole carbon and energy source, maltose. In aspergilli and other mold fungi, asexual reproduction through formation of elaborate conidiogenic structures normally requires an aerial interface. This requirement is bypassed in submerged culture in response to severe nutrient limitation. Continuous cultures with cell retention (retentostat cultures) were applied to generate a fundamental physiological state, where the specific growth rate approaches zero, as the density of the cell population adapts to the supply of the limiting energy source. Temporal differentiation of mycelium structure and commitment to asexual reproduction were major phenomena, apparent on biochemical, morphological, physiological, and transcriptomic level. The severe substrate limitation had a rapid negative impact on cytoplasmic processes, and promoted endo- and exogenous nutrient mobilization, and hyphal compartmentalisation. The first conidiogenic structures appeared after one day with little additional differentiation until Day 4 to 6, where a transition to full commitment to reproductive growth took place. Submerged conidiation in A. niger involved transcriptional regulation of homologs of the regulatory pathway, centered around the Bristle gene (brlA), and structural genes previously described in other aspergilli. Comparison of transcriptomes, revealed a number of co-regulated gene clusters, which appear to encode secondary metabolite biosynthetic potential. We discuss the concept of maintenance energy in the context of differentiation, a possible physiological trigger for sporulation and the special physiological adaptations of the starved mycelium. We also present a simple and efficient method for in situ retention of filamentous organisms. The dataset consists of 9 Affymetrix arrays derived from defined growth conditions of lab-scale bioreactor cultures (5L). Total RNA was extracted from biomass harvested at three different growth phases: exponential growth phase, 2 and 8 days of retentostat cultivation. For each of the phases, the data is derived from three biological replicates.

ORGANISM(S): Aspergillus niger  

SUBMITTER: Gerda E Lamers   Benjamin M Nitsche  Mark Arentshorst  Cees A Hondel  Arthur F Ram  Benjamin M. Nitsche  Thomas R Jørgensen 

PROVIDER: E-GEOD-21752 | ArrayExpress | 2010-07-07

SECONDARY ACCESSION(S): GSE21752PRJNA127343

REPOSITORIES: GEO, ArrayExpress

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Publications

Transcriptomic insights into the physiology of Aspergillus niger approaching a specific growth rate of zero.

Jørgensen Thomas R TR   Nitsche Benjamin M BM   Lamers Gerda E GE   Arentshorst Mark M   van den Hondel Cees A CA   Ram Arthur F AF  

Applied and environmental microbiology 20100618 16


The physiology of filamentous fungi at growth rates approaching zero has been subject to limited study and exploitation. With the aim of uncoupling product formation from growth, we have revisited and improved the retentostat cultivation method for Aspergillus niger. A new retention device was designed allowing reliable and nearly complete cell retention even at high flow rates. Transcriptomic analysis was used to explore the potential for product formation at very low specific growth rates. The  ...[more]

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