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Spatial differentiation of gene expression in Aspergillus niger colonies grown for sugar beet pulp utilization

ABSTRACT: Filamentous fungi are ubiquitous organisms and major plant biomass degraders. As a single colony, some fungal species can colonize large areas as up to five soccer stadia. During growth, the mycelium encounters heterogeneous carbon sources. Here we assessed whether substrate heterogeneity is a main determinant of spatial gene expression in colonies of Aspergillus niger. This question was addressed by analyzing whole-genome gene expression in five concentric zones of 5-day-old sugar beet pulp grown colonies. Growth, protein production and secretion were occurring throughout the whole colony. Carbon and nitrate utilization were constant from the centre to the periphery whereas genes encoding plant cell wall degrading enzymes were expressed with a different pattern across the colony. Finally our results demonstrate a fine-tuning of the different enzymatic tools available in A. niger and expand the knowledge on how this fungus adapts as it colonizes complex environments.

ORGANISM(S): Aspergillus niger Aspergillus niger CBS 513.88

PROVIDER: GSE66641 | GEO | 2016/03/04

SECONDARY ACCESSION(S): PRJNA277532

REPOSITORIES: GEO

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Project description:Background: Sugar beet is an important root crop, accounting for 30 % of the sugar production worldwide. The long growing season make sugar beets exposed to a range of plant pathogens for longer periods than most other crops. Here, contrasting sugar beet genotypes were used for transcriptome analysis to reveal differential responses and new defense genes to Rhizoctonia solani, a soilborn fungal pathogen. Results: After curation of primary RNA-sequencing reads, 16,768 genes deriving from 36 samples composed of two susceptible and two resistant sugar beet genotypes, three time-points (0, two and five days post inoculation), each in three replicates were subjected for analysis. Among the elevated 217 transcripts at 2 dpi, three resistance-like genes (Bv4_088600_cumk, Bv8u_204980_frqg, and Bv_44840_iifo) were activated. By employing edgeR package statistics, 660 genes were significantly different (false discovery rate < 0.05) between resistant and susceptible genotypes in their response to R. solani inoculation. A combination of eukaryotic orthologous group assignments and gene ontology enrichment analyses, revealed three Bet v I/Major latex protein homologous genes (Bv7_162510_pymu, Bv7_162520_etow, Bv_27270_xeas) in the resistant genotypes after five days of fungal challenge. Co-expression network analysis of differentially expressed sugar beet genes further identified a MYB46 transcription factor, a plant disease resistance response protein (DRR206) and a flavonoid o-methyltransferase protein. MYB46 has a key function in secondary cell wall formation and exist as a singleton in the sugar beet genome. The genome of R. solani is enriched in cell wall degrading enzyme encoding genes and it is anticipated that they represent important virulence factors. Compared to Arabidopsis thaliana, sugar beet has 2.4-fold more carbohydrate esterases and particularly large numbers (26-fold) of auxiliary activity encoding genes whose function in cell wall biosynthesis is largely unknown. Conclusions: Based on components identified in this sugar beet transcript data set we conclude that defense responses to R. solani are attributed to a wide range of gene categories but functional information is missing to a large extent. This calls for careful integration to avoid negative side effects to obtain optimal combinations of these traits in order to reach the long-term goal of improved resistance in sugar beet.

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Spatial differentiation of gene expression in Aspergillus niger colonies grown for sugar beet pulp utilization

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