PXD002130

PXD002130 is an original dataset announced via ProteomeXchange.

Title	Spatial differentiation of gene expression in Aspergillus niger colony grown for sugar beet pulp utilization
Description	Degradation of plant biomass to fermentable sugars is of critical importance for the use of plant materials for biofuels. Filamentous fungi are ubiquitous organisms and major plant biomass degraders. Single colonies of some fungal species can colonize massive areas as large as five soccer stadia.During growth, the mycelium encounters heterogeneous carbon sources. Here we assessed whether substrate heterogeneity is a major determinant of spatial gene expression in colonies of Aspergillus niger. We analyzed whole-genome gene expression in five concentric zones of 5-day-old colonies utilizing sugar beet pulp as a complex carbon source. Growth, protein production and secretion occurred throughout the colony. Genes involved in carbon catabolism and nitrate utilization were expressed uniformly from the centre to the periphery whereas genes encoding plant biomass degrading enzymes were expressed differentially across the colony. A combined adaptive response of carbon-catabolism and enzyme production to locally available monosaccharides was observed. Finally, our results demonstrate a fine-tuning of the different enzymatic tools available in A. niger and reveal how this fungus adapts as it colonizes complex environments.
HostingRepository	PRIDE
AnnounceDate	2015-09-09
AnnouncementXML	Submission_2015-09-09_06:36:00.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Harm Post
SpeciesList	scientific name: Aspergillus niger; NCBI TaxID: 5061;
ModificationList	monohydroxylated residue; carbamoylated residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2015-04-30 08:16:55	ID requested
⏵ 1	2015-09-09 06:36:01	announced

Benoit I, Zhou M, Vivas Duarte A, Downes DJ, Todd RB, Kloezen W, Post H, Heck AJ, Maarten Altelaar AF, de Vries RP, Spatial differentiation of gene expression in Aspergillus niger colony grown for sugar beet pulp utilization. Sci Rep, 5():13592(2015) [pubmed]

curator keyword: Biological

submitter keyword: Aspergillus niger, plant biomass degrading enzymes, spatial gene expression, heterogeneity

sugar beet pulp

Ronald Peter de Vries
contact affiliation	Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre Institute of the Royal Netherlands Academy of Arts and Sciences(KNAW) Fungal Molecular Physiology, Utrecht University, The Netherlands
contact email	r.devries@cbs.knaw.nl
lab head
Harm Post
contact affiliation	Biomolecular Mass Spectrometry and Proteomics Group
contact email	h.post@uu.nl
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD002130

PRIDE project URI

• PRIDE
  1. PXD002130
     1. Label: PRIDE project
     2. Name: Spatial differentiation of gene expression in Aspergillus niger colony grown for sugar beet pulp utilization